Homo sapiens complex locus ABLIM1, encoding actin binding LIM protein 1.
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SUMMARY back to top
RefSeq summary
[ABLIM1] This gene encodes a cytoskeletal LIM protein that binds to actin filaments via a domain that is homologous to erythrocyte dematin. LIM domains, found in over 60 proteins, play key roles in the regulation of developmental pathways. LIM domains also function as protein-binding interfaces, mediating specific protein-protein interactions. The protein encoded by this gene could mediate such interactions between actin filaments and cytoplasmic targets. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq].

RefSeq annotates 4 representative transcripts, but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 23 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at high level, 2.1 times the average gene in this release. The sequence of this gene is defined by 235 GenBank accessions from 227 cDNA clones, some from brain (seen 34 times), testis (23), normal nasopharynx (11), human skeletal muscle (10), cerebellum (9), uterus (6), islets of langerhans (5) and 54 other tissues. We annotate structural defects or features in 41 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 41 distinct introns (40 gt-ag, 1 gc-ag). Transcription produces 32 different mRNAs, 23 alternatively spliced variants and 9 unspliced forms. There are 18 probable alternative promotors, 7 non overlapping alternative last exons and 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 7 cassette exons, overlapping exons with different boundaries.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant eAug10).
Function: There are 14 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Alzheimer Disease; Neoplasms), proposed to participate in pathway (Axon guidance) and a process (cytoskeleton organization). Proteins are expected to have molecular functions (actin binding, metal ion binding, zinc ion binding) and to localize in various compartments (nucleus, cytoplasm). Putative protein interactors have been described (ACTG1, BEGAIN, CALCOCO2, GOLGA2, HOOK2, KCNJ12, KRT15, LDOC1, SFN, TRAF2, TSC22D4ANDC7ORF61, USHBP1ANDNR2F6, VIM, YWHAG).
Protein coding potential: 20 spliced and the unspliced mRNAs putatively encode good proteins, altogether 21 different isoforms (5 complete, 3 COOH complete, 13 partial), some containing LIM domain [Pfam], a second peroximal domain, a coiled coil stretch [Psort2]. The remaining 11 mRNA variants (3 spliced, 8 unspliced; 7 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by acetylation; o-glcnac; phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 10, links to other databases and other names
Map: This gene ABLIM1 maps on chromosome 10, at 10q25 according to Entrez Gene. In AceView, it covers 332.98 kb, from 116528019 to 116195042 (NCBI 37, August 2010), on the reverse strand.
Links to: , manual annotations from GAD, KEGG_04360, PhosphoSite, the SNP view, gene overviews from Entrez Gene 3983, GeneCards, expression data from ECgene, UniGene Hs.438236, Hs.538331, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as ABLIM1, RP11-317F20.1, ABLIM, LIMAB1, LIMATIN, MGC1224, FLJ14564, KIAA0059, DKFZp781D0148, LOC3983, dushu or klawjybu, speejybu. It has been described as actin-binding LIM protein 1, abLIM-1, OTTHUMP00000020532, OTTHUMP00000020533, OTTHUMP00000020534, OTTHUMP00000020535, OTTHUMP00000020537, LIM actin-binding protein 1, actin-binding double zinc finger protein, actin-binding double-zinc-finger protein, actin-binding LIM protein family member 1.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Ablim1 (e=2 10-29).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene unc-115 (e=0.007), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene NMT1.1 (e=0.41), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
ABLIM1 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 28.5 106 65.5 16.4 75.3 21.6 21.6 75.3 114 281 99.3 24.8 46.3 199 12.4 5.04 14.3 16.4 14.3 32.8 35.1 20.2 18.8 28.5 151 32.8 161 26.6 75.3 49.7 75.3 61.1 10.8 173 24.8 70.2 11.6 10.8 23.2 21.6 245 40.3 61.1 323 46.3 46.3 140 92.7 57.1 213 49.7 20.2 61.1 86.5 346 26.6 70.2 53.2 10.8 49.7 32.8 199 106 32.8 37.6 10.1 40.3 32.8 185 30.6 37.6 199 32.8 75.3 65.5 114 32.8 10.1 49.7 37.6 32.8 14.3 49.7 65.5 35.1 106 46.3 346 99.3 70.2 37.6 57.1 397 32.8 43.2 40.3 140 24.8 80.7 65.5 13.3 92.7 86.5 346 26.6 30.6 24.8 86.5 32.8 35.1 40.3 46.3 30.6 99.3 17.6 35.1 99.3 17.6 57.1 35.1 199 92.7 323 49.7 397 57.1 80.7 65.5 40.3 80.7 99.3 46.3 40.3 173 40.3 30.6 5.79 15.3 32.8 37.6 49.7 371 32.8 32.8 40.3 18.8 49.7 37.6 21.6 17.6 35.1 245 46.3 92.7 53.2 61.1 57.1 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
Read more...
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene ABLIM1 5' 3' encoded on minus strand of chromosome 10 from 116,528,019 to 116,195,042 14 23366 25759 1948 47538 15860 32085 a 3 25759 61017 47538 464 b 1 23366 n 3 61017 47538 9810 32085 c 9 23366 vf 25759 61017 47538 15860 d 9020 k vc-u 61017 47538 39260 e 9020 23366 f 2 s 39260 u va-u 2 204 23366 g t r 8451 23366 l 2983 61017 47538 h 920 23366 i vb-u vh-u 1 23366 j m 5 23366 o q-u ve-u vk-u vi-u 5 23366 p 1 87 vd 5 23366 vg vj-u 10kb 0 96 bp exon 11695 bp [gt-ag] intron 13 GenBank accessions 1 RNA-seq supporting reads 1 Blood 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 184 bp exon 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 23520 bp [gt-ag] intron 36 GenBank accessions 25503 RNA-seq supporting reads 393 UHR pooled cells 10999 Brain 909 Blood 12833 Neuroblastoma 369 Other (also 17382 Primates bodymap) 127 bp exon 2551 bp [gt-ag] intron 19 GenBank accessions 20794 RNA-seq supporting reads 336 UHR pooled cells 8985 Brain 434 Blood 10568 Neuroblastoma 471 Other (also 12700 Primates bodymap) 94 bp exon 53126 bp [gt-ag] intron 16 GenBank accessions 25743 RNA-seq supporting reads 392 UHR pooled cells 11234 Brain 719 Blood 12971 Neuroblastoma 427 Other (also 13772 Primates bodymap) 88 bp exon 3774 bp [gt-ag] intron 88 GenBank accessions 70184 RNA-seq supporting reads 3273 UHR pooled cells 28157 Brain 15709 Blood 22475 Neuroblastoma 570 Other (also 32517 Primates bodymap) 59 bp exon 14825 bp [gt-ag] intron 8 GenBank accessions 1940 RNA-seq supporting reads 485 UHR pooled cells 433 Brain 482 Blood 538 Neuroblastoma 2 Other (also 231 Primates bodymap) 156 bp exon 4760 bp [gt-ag] intron 56 GenBank accessions 47353 RNA-seq supporting reads 2364 UHR pooled cells 18848 Brain 9392 Blood 16325 Neuroblastoma 424 Other (also 19910 Primates bodymap) 36 bp exon 2353 bp [gt-ag] intron 50 GenBank accessions 49781 RNA-seq supporting reads 2584 UHR pooled cells 19585 Brain 9924 Blood 17241 Neuroblastoma 447 Other (also 21677 Primates bodymap) 130 bp exon 14026 bp [gt-ag] intron 38 GenBank accessions 47500 RNA-seq supporting reads 4050 UHR pooled cells 8336 Brain 10468 Blood 24129 Neuroblastoma 517 Other (also 17176 Primates bodymap) 48 bp exon 3603 bp [gt-ag] intron 33 GenBank accessions 15827 RNA-seq supporting reads 1689 UHR pooled cells 327 Brain 8990 Blood 4761 Neuroblastoma 60 Other (also 4617 Primates bodymap) 141 bp exon 2476 bp [gt-ag] intron 36 GenBank accessions 32049 RNA-seq supporting reads 4489 UHR pooled cells 1856 Brain 8472 Blood 16902 Neuroblastoma 330 Other (also 10146 Primates bodymap) 92 bp exon 1177 bp [gt-ag] intron 42 GenBank accessions 72067 RNA-seq supporting reads 3640 UHR pooled cells 30131 Brain 12866 Blood 24685 Neuroblastoma 745 Other (also 33814 Primates bodymap) 106 bp exon 2242 bp [gt-ag] intron 39 GenBank accessions 80186 RNA-seq supporting reads 3751 UHR pooled cells 33679 Brain 16041 Blood 25955 Neuroblastoma 760 Other (also 24596 Primates bodymap) 65 bp exon 644 bp [gt-ag] intron 32 GenBank accessions 76453 RNA-seq supporting reads 3683 UHR pooled cells 32617 Brain 14601 Blood 24989 Neuroblastoma 563 Other (also 29985 Primates bodymap) 61 bp exon 927 bp [gt-ag] intron 1 GenBank accession 49201 RNA-seq supporting reads 2654 UHR pooled cells 22028 Brain 7889 Blood 16244 Neuroblastoma 386 Other (also 27897 Primates bodymap) 462 bp exon 30 accessions, some from testis (seen 11 times) amygdala (2), colon (once) epidermis (once), head neck (once) capped 5' end, 9 accessions 462 bp exon 136 bp exon 14483 bp [gt-ag] intron 3 GenBank accessions 184 bp exon 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 23520 bp [gt-ag] intron 36 GenBank accessions 25503 RNA-seq supporting reads 393 UHR pooled cells 10999 Brain 909 Blood 12833 Neuroblastoma 369 Other (also 17382 Primates bodymap) 127 bp exon 2551 bp [gt-ag] intron 19 GenBank accessions 20794 RNA-seq supporting reads 336 UHR pooled cells 8985 Brain 434 Blood 10568 Neuroblastoma 471 Other (also 12700 Primates bodymap) 94 bp exon 53126 bp [gt-ag] intron 16 GenBank accessions 25743 RNA-seq supporting reads 392 UHR pooled cells 11234 Brain 719 Blood 12971 Neuroblastoma 427 Other (also 13772 Primates bodymap) 88 bp exon 3774 bp [gt-ag] intron 88 GenBank accessions 70184 RNA-seq supporting reads 3273 UHR pooled cells 28157 Brain 15709 Blood 22475 Neuroblastoma 570 Other (also 32517 Primates bodymap) 59 bp exon 14001 bp [gt-ag] intron 71 GenBank accessions 60946 RNA-seq supporting reads 2372 UHR pooled cells 23801 Brain 15722 Blood 18624 Neuroblastoma 427 Other (also 22903 Primates bodymap) 78 bp exon 746 bp [gt-ag] intron 78 GenBank accessions 65801 RNA-seq supporting reads 3000 UHR pooled cells 29024 Brain 11799 Blood 21374 Neuroblastoma 604 Other (also 31695 Primates bodymap) 156 bp exon 4760 bp [gt-ag] intron 56 GenBank accessions 47353 RNA-seq supporting reads 2364 UHR pooled cells 18848 Brain 9392 Blood 16325 Neuroblastoma 424 Other (also 19910 Primates bodymap) 36 bp exon 2353 bp [gt-ag] intron 50 GenBank accessions 49781 RNA-seq supporting reads 2584 UHR pooled cells 19585 Brain 9924 Blood 17241 Neuroblastoma 447 Other (also 21677 Primates bodymap) 130 bp exon 14026 bp [gt-ag] intron 38 GenBank accessions 47500 RNA-seq supporting reads 4050 UHR pooled cells 8336 Brain 10468 Blood 24129 Neuroblastoma 517 Other (also 17176 Primates bodymap) 48 bp exon 1488 bp [gt-ag] intron 6 GenBank accessions 458 RNA-seq supporting reads 5 UHR pooled cells 1 Brain 396 Blood 56 Neuroblastoma (also 8 Primates bodymap) 57 bp exon 9 accessions, some from germinal center B cell (seen 3 times) brain (once), medulla (once) testis (once) capped 5' end, 1 accession Validated 3' end, 4 accessions 57 bp exon 189 bp exon 59434 bp [gt-ag] intron 1 GenBank accession 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 109 bp exon 1 accession from testis 109 bp exon 46 bp exon 9594 bp [gc-ag] intron 3 GenBank accessions 249 bp exon 34781 bp [gt-ag] intron 56 GenBank accessions 35337 RNA-seq supporting reads 2321 UHR pooled cells 12964 Brain 13529 Blood 6392 Neuroblastoma 131 Other (also 13459 Primates bodymap) 88 bp exon 88 bp exon 3774 bp [gt-ag] intron 88 GenBank accessions 70184 RNA-seq supporting reads 3273 UHR pooled cells 28157 Brain 15709 Blood 22475 Neuroblastoma 570 Other (also 32517 Primates bodymap) 59 bp exon 14001 bp [gt-ag] intron 71 GenBank accessions 60946 RNA-seq supporting reads 2372 UHR pooled cells 23801 Brain 15722 Blood 18624 Neuroblastoma 427 Other (also 22903 Primates bodymap) 78 bp exon 746 bp [gt-ag] intron 78 GenBank accessions 65801 RNA-seq supporting reads 3000 UHR pooled cells 29024 Brain 11799 Blood 21374 Neuroblastoma 604 Other (also 31695 Primates bodymap) 156 bp exon 4760 bp [gt-ag] intron 56 GenBank accessions 47353 RNA-seq supporting reads 2364 UHR pooled cells 18848 Brain 9392 Blood 16325 Neuroblastoma 424 Other (also 19910 Primates bodymap) 36 bp exon 2353 bp [gt-ag] intron 50 GenBank accessions 49781 RNA-seq supporting reads 2584 UHR pooled cells 19585 Brain 9924 Blood 17241 Neuroblastoma 447 Other (also 21677 Primates bodymap) 130 bp exon 14026 bp [gt-ag] intron 38 GenBank accessions 47500 RNA-seq supporting reads 4050 UHR pooled cells 8336 Brain 10468 Blood 24129 Neuroblastoma 517 Other (also 17176 Primates bodymap) 48 bp exon 3597 bp [gt-ag] intron 4 GenBank accessions 9806 RNA-seq supporting reads 1364 UHR pooled cells 832 Brain 971 Blood 6474 Neuroblastoma 165 Other (also 3255 Primates bodymap) 147 bp exon 2476 bp [gt-ag] intron 36 GenBank accessions 32049 RNA-seq supporting reads 4489 UHR pooled cells 1856 Brain 8472 Blood 16902 Neuroblastoma 330 Other (also 10146 Primates bodymap) 92 bp exon 1177 bp [gt-ag] intron 42 GenBank accessions 72067 RNA-seq supporting reads 3640 UHR pooled cells 30131 Brain 12866 Blood 24685 Neuroblastoma 745 Other (also 33814 Primates bodymap) 106 bp exon 2242 bp [gt-ag] intron 39 GenBank accessions 80186 RNA-seq supporting reads 3751 UHR pooled cells 33679 Brain 16041 Blood 25955 Neuroblastoma 760 Other (also 24596 Primates bodymap) 65 bp exon 644 bp [gt-ag] intron 32 GenBank accessions 76453 RNA-seq supporting reads 3683 UHR pooled cells 32617 Brain 14601 Blood 24989 Neuroblastoma 563 Other (also 29985 Primates bodymap) 17 bp exon 24 accessions, some from nervous normal (seen 3 times) testis (3), burkitt lymphoma (2) lymph (2), thymus (2) 17 bp exon 310 bp exon 310 bp exon 310 bp exon 67317 bp [gt-ag] intron 1 GenBank accession 8 RNA-seq supporting reads 8 Brain (also 1 Primates bodymap) 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 1 accession from brain capped 5' end, 1 accession 130 bp exon 217 bp exon 217 bp exon 53126 bp [gt-ag] intron 16 GenBank accessions 25743 RNA-seq supporting reads 392 UHR pooled cells 11234 Brain 719 Blood 12971 Neuroblastoma 427 Other (also 13772 Primates bodymap) 88 bp exon 3774 bp [gt-ag] intron 88 GenBank accessions 70184 RNA-seq supporting reads 3273 UHR pooled cells 28157 Brain 15709 Blood 22475 Neuroblastoma 570 Other (also 32517 Primates bodymap) 59 bp exon 14001 bp [gt-ag] intron 71 GenBank accessions 60946 RNA-seq supporting reads 2372 UHR pooled cells 23801 Brain 15722 Blood 18624 Neuroblastoma 427 Other (also 22903 Primates bodymap) 78 bp exon 746 bp [gt-ag] intron 78 GenBank accessions 65801 RNA-seq supporting reads 3000 UHR pooled cells 29024 Brain 11799 Blood 21374 Neuroblastoma 604 Other (also 31695 Primates bodymap) 156 bp exon 4760 bp [gt-ag] intron 56 GenBank accessions 47353 RNA-seq supporting reads 2364 UHR pooled cells 18848 Brain 9392 Blood 16325 Neuroblastoma 424 Other (also 19910 Primates bodymap) 36 bp exon 2353 bp [gt-ag] intron 50 GenBank accessions 49781 RNA-seq supporting reads 2584 UHR pooled cells 19585 Brain 9924 Blood 17241 Neuroblastoma 447 Other (also 21677 Primates bodymap) 130 bp exon 14026 bp [gt-ag] intron 38 GenBank accessions 47500 RNA-seq supporting reads 4050 UHR pooled cells 8336 Brain 10468 Blood 24129 Neuroblastoma 517 Other (also 17176 Primates bodymap) 48 bp exon 3603 bp [gt-ag] intron 33 GenBank accessions 15827 RNA-seq supporting reads 1689 UHR pooled cells 327 Brain 8990 Blood 4761 Neuroblastoma 60 Other (also 4617 Primates bodymap) 2 accessions, some from brain (seen once) synovial membrane tissue from rheumatioidarthritis (once) whole brain (once) 140 bp exon 200 bp exon 200 bp exon 166099 bp [gt-ag] intron 4 GenBank accessions 9016 RNA-seq supporting reads 67 UHR pooled cells 3630 Brain 10 Blood 5223 Neuroblastoma 86 Other (also 1737 Primates bodymap) 680 bp exon 1 accession from brain 680 bp exon 947 bp exon 947 bp exon 2 accessions, some from eyeball (seen once) pooled-skin (once) 947 bp exon 276 bp exon 276 bp exon 39 bp uORF 276 bp exon 34781 bp [gt-ag] intron 56 GenBank accessions 35337 RNA-seq supporting reads 2321 UHR pooled cells 12964 Brain 13529 Blood 6392 Neuroblastoma 131 Other (also 13459 Primates bodymap) 88 bp exon 88 bp exon 88 bp exon 3774 bp [gt-ag] intron 88 GenBank accessions 70184 RNA-seq supporting reads 3273 UHR pooled cells 28157 Brain 15709 Blood 22475 Neuroblastoma 570 Other (also 32517 Primates bodymap) 59 bp exon 59 bp exon 14001 bp [gt-ag] intron 71 GenBank accessions 60946 RNA-seq supporting reads 2372 UHR pooled cells 23801 Brain 15722 Blood 18624 Neuroblastoma 427 Other (also 22903 Primates bodymap) 78 bp exon 78 bp exon 746 bp [gt-ag] intron 78 GenBank accessions 65801 RNA-seq supporting reads 3000 UHR pooled cells 29024 Brain 11799 Blood 21374 Neuroblastoma 604 Other (also 31695 Primates bodymap) 156 bp exon 156 bp exon 4760 bp [gt-ag] intron 56 GenBank accessions 47353 RNA-seq supporting reads 2364 UHR pooled cells 18848 Brain 9392 Blood 16325 Neuroblastoma 424 Other (also 19910 Primates bodymap) 36 bp exon 36 bp exon 2353 bp [gt-ag] intron 50 GenBank accessions 49781 RNA-seq supporting reads 2584 UHR pooled cells 19585 Brain 9924 Blood 17241 Neuroblastoma 447 Other (also 21677 Primates bodymap) 130 bp exon 130 bp exon 14026 bp [gt-ag] intron 38 GenBank accessions 47500 RNA-seq supporting reads 4050 UHR pooled cells 8336 Brain 10468 Blood 24129 Neuroblastoma 517 Other (also 17176 Primates bodymap) 48 bp exon 48 bp exon 6220 bp [gt-ag] intron 6 GenBank accessions 39254 RNA-seq supporting reads 203 UHR pooled cells 25350 Brain 351 Blood 12932 Neuroblastoma 418 Other (also 17725 Primates bodymap) 92 bp exon 92 bp exon 1177 bp [gt-ag] intron 42 GenBank accessions 72067 RNA-seq supporting reads 3640 UHR pooled cells 30131 Brain 12866 Blood 24685 Neuroblastoma 745 Other (also 33814 Primates bodymap) 106 bp exon 106 bp exon 2242 bp [gt-ag] intron 39 GenBank accessions 80186 RNA-seq supporting reads 3751 UHR pooled cells 33679 Brain 16041 Blood 25955 Neuroblastoma 760 Other (also 24596 Primates bodymap) 65 bp exon 65 bp exon 644 bp [gt-ag] intron 32 GenBank accessions 76453 RNA-seq supporting reads 3683 UHR pooled cells 32617 Brain 14601 Blood 24989 Neuroblastoma 563 Other (also 29985 Primates bodymap) 40 bp exon 40 bp exon 35 accessions, some from human skeletal muscle (seen 6 times) brain (4), cerebellum (4) normal nasopharynx (4) lymph (2) 40 bp exon 147 bp exon 147 bp exon 166099 bp [gt-ag] intron 4 GenBank accessions 9016 RNA-seq supporting reads 67 UHR pooled cells 3630 Brain 10 Blood 5223 Neuroblastoma 86 Other (also 1737 Primates bodymap) 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 23520 bp [gt-ag] intron 36 GenBank accessions 25503 RNA-seq supporting reads 393 UHR pooled cells 10999 Brain 909 Blood 12833 Neuroblastoma 369 Other (also 17382 Primates bodymap) 127 bp exon 4 accessions, some from brain (seen 2 times) lung normal (once), medulla (once) whole brain (once) 127 bp exon 88 bp exon 88 bp exon 3774 bp [gt-ag] intron 88 GenBank accessions 70184 RNA-seq supporting reads 3273 UHR pooled cells 28157 Brain 15709 Blood 22475 Neuroblastoma 570 Other (also 32517 Primates bodymap) 59 bp exon 8799 bp [gt-ag] intron 1 GenBank accession 1 RNA-seq supporting reads 1 Blood (also 2 Primates bodymap) 1 accession 76 bp exon 70 bp exon 1707 bp [gt-ag] intron 9 GenBank accessions 18374 RNA-seq supporting reads 97 UHR pooled cells 15033 Brain 312 Blood 2853 Neuroblastoma 79 Other (also 9523 Primates bodymap) 48 bp exon 6220 bp [gt-ag] intron 6 GenBank accessions 39254 RNA-seq supporting reads 203 UHR pooled cells 25350 Brain 351 Blood 12932 Neuroblastoma 418 Other (also 17725 Primates bodymap) 37 bp exon 1 accession from nervous normal 37 bp exon 1085 bp exon 1085 bp exon 9 accessions, some from brain (seen 2 times) hippocampus (2), human skeletal muscle (once) liver (once), pooled human melanocyte fetal heart, andpregnant uterus (once) capped 5' end, 4 accessions 1085 bp exon 114 bp exon 69246 bp [gt-ag] intron 1 GenBank accession 1 RNA-seq supporting reads 1 Brain 119 bp exon 119 bp exon 12963 bp [gt-ag] intron 1 GenBank accession 203 RNA-seq supporting reads 2 UHR pooled cells 96 Brain 1 Blood 101 Neuroblastoma 3 Other (also 1 Primates bodymap) 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 23520 bp [gt-ag] intron 36 GenBank accessions 25503 RNA-seq supporting reads 393 UHR pooled cells 10999 Brain 909 Blood 12833 Neuroblastoma 369 Other (also 17382 Primates bodymap) 286 bp exon 3 accessions, some from islets of langerhans (seen 2 times) pancreas (2), thymus (once) capped 5' end, 1 accession 286 bp exon 85 bp exon 2353 bp [gt-ag] intron 50 GenBank accessions 49781 RNA-seq supporting reads 2584 UHR pooled cells 19585 Brain 9924 Blood 17241 Neuroblastoma 447 Other (also 21677 Primates bodymap) 869 bp exon 4 accessions, some from breast normal (seen 2 times) embryonic stem (once) uterus (once), well-differentiated endometrialadenocarcinoma 7 pooled tumors (once) 869 bp exon 1505 bp exon 1505 bp exon 54 bp uORF 1505 bp exon 1505 bp exon 1177 bp [gt-ag] intron 42 GenBank accessions 72067 RNA-seq supporting reads 3640 UHR pooled cells 30131 Brain 12866 Blood 24685 Neuroblastoma 745 Other (also 33814 Primates bodymap) 106 bp exon 106 bp exon 2242 bp [gt-ag] intron 39 GenBank accessions 80186 RNA-seq supporting reads 3751 UHR pooled cells 33679 Brain 16041 Blood 25955 Neuroblastoma 760 Other (also 24596 Primates bodymap) 65 bp exon 65 bp exon 644 bp [gt-ag] intron 32 GenBank accessions 76453 RNA-seq supporting reads 3683 UHR pooled cells 32617 Brain 14601 Blood 24989 Neuroblastoma 563 Other (also 29985 Primates bodymap) 18 bp exon 5 accessions, some from breast carcinoma (seen once) cerebellum (once), colon (once) kidney (once), t-lymphocytes (once) capped 5' end, 2 accessions 18 bp exon 864 bp exon 864 bp exon 29940 bp [gt-ag] intron 20 GenBank accessions 8431 RNA-seq supporting reads 186 UHR pooled cells 3763 Brain 522 Blood 3921 Neuroblastoma 39 Other (also 6508 Primates bodymap) 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 24 accessions, some from brain (seen 13 times) islets of langerhans (3) pancreas (3), cerebellum (2) esophageal, tumor tissue (once) 110 bp exon 270 bp exon 34760 bp [gt-ag] intron 9 GenBank accessions 2974 RNA-seq supporting reads 275 UHR pooled cells 823 Brain 1154 Blood 716 Neuroblastoma 6 Other (also 62 Primates bodymap) 88 bp exon 88 bp exon 3774 bp [gt-ag] intron 88 GenBank accessions 70184 RNA-seq supporting reads 3273 UHR pooled cells 28157 Brain 15709 Blood 22475 Neuroblastoma 570 Other (also 32517 Primates bodymap) 59 bp exon 14001 bp [gt-ag] intron 71 GenBank accessions 60946 RNA-seq supporting reads 2372 UHR pooled cells 23801 Brain 15722 Blood 18624 Neuroblastoma 427 Other (also 22903 Primates bodymap) 78 bp exon 746 bp [gt-ag] intron 78 GenBank accessions 65801 RNA-seq supporting reads 3000 UHR pooled cells 29024 Brain 11799 Blood 21374 Neuroblastoma 604 Other (also 31695 Primates bodymap) 156 bp exon 4760 bp [gt-ag] intron 56 GenBank accessions 47353 RNA-seq supporting reads 2364 UHR pooled cells 18848 Brain 9392 Blood 16325 Neuroblastoma 424 Other (also 19910 Primates bodymap) 36 bp exon 2353 bp [gt-ag] intron 50 GenBank accessions 49781 RNA-seq supporting reads 2584 UHR pooled cells 19585 Brain 9924 Blood 17241 Neuroblastoma 447 Other (also 21677 Primates bodymap) 130 bp exon 14026 bp [gt-ag] intron 38 GenBank accessions 47500 RNA-seq supporting reads 4050 UHR pooled cells 8336 Brain 10468 Blood 24129 Neuroblastoma 517 Other (also 17176 Primates bodymap) 33 bp exon 11 accessions, some from brain (seen 3 times) normal nasopharynx (3) neuroblastoma (2), cerebellum (once) human skeletal muscle (once) 33 bp exon 366 bp exon 366 bp exon 82328 bp [gt-ag] intron 8 GenBank accessions 912 RNA-seq supporting reads 32 UHR pooled cells 128 Brain 748 Neuroblastoma 4 Other (also 3665 Primates bodymap) 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 23520 bp [gt-ag] intron 36 GenBank accessions 25503 RNA-seq supporting reads 393 UHR pooled cells 10999 Brain 909 Blood 12833 Neuroblastoma 369 Other (also 17382 Primates bodymap) 12 bp exon 4 accessions, some from bladder (seen once) human skeletal muscle (once) uterus (once) capped 5' end, 3 accessions 12 bp exon 1053 bp exon 1053 bp exon 3 accessions, some from sympathetic trunk (seen 2 times) 1053 bp exon 506 bp exon 2 accessions, some from breast normal (seen once) head neck (once) 506 bp exon 53 bp exon 53 bp exon 8011 bp [gt-ag] intron 1 GenBank accession 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 23520 bp [gt-ag] intron 36 GenBank accessions 25503 RNA-seq supporting reads 393 UHR pooled cells 10999 Brain 909 Blood 12833 Neuroblastoma 369 Other (also 17382 Primates bodymap) 1 accession from thymus capped 5' end, 1 accession 56 bp exon 256 bp exon 256 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 23520 bp [gt-ag] intron 36 GenBank accessions 25503 RNA-seq supporting reads 393 UHR pooled cells 10999 Brain 909 Blood 12833 Neuroblastoma 369 Other (also 17382 Primates bodymap) 127 bp exon 2551 bp [gt-ag] intron 19 GenBank accessions 20794 RNA-seq supporting reads 336 UHR pooled cells 8985 Brain 434 Blood 10568 Neuroblastoma 471 Other (also 12700 Primates bodymap) 54 bp exon 1 accession from trachea capped 5' end, 1 accession 54 bp exon 17 bp exon 96844 bp [gt-ag] intron 1 GenBank accession 4 RNA-seq supporting reads 3 Brain 1 Neuroblastoma 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 184 bp exon 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 23520 bp [gt-ag] intron 36 GenBank accessions 25503 RNA-seq supporting reads 393 UHR pooled cells 10999 Brain 909 Blood 12833 Neuroblastoma 369 Other (also 17382 Primates bodymap) 102 bp exon 1 accession from placenta capped 5' end, 1 accession 102 bp exon 539 bp exon 539 bp exon 3 accessions, some from kidney (seen once) placenta normal (once) 539 bp exon 674 bp exon 674 bp exon 1 accession 674 bp exon 366 bp exon 0 accession 366 bp exon 494 bp exon 2 accessions, some from placenta (seen once) Validated 3' end, 1 accession 494 bp exon 60 bp uORF 101 bp exon 101 bp exon 10087 bp [gt-ag] intron 5 GenBank accessions 135 bp exon 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 184 bp exon 184 bp exon 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 110 bp exon 110 bp exon 23520 bp [gt-ag] intron 36 GenBank accessions 25503 RNA-seq supporting reads 393 UHR pooled cells 10999 Brain 909 Blood 12833 Neuroblastoma 369 Other (also 17382 Primates bodymap) 42 bp exon 42 bp exon 5 accessions, some from testis (seen 5 times) capped 5' end, 5 accessions 42 bp exon 416 bp exon 416 bp exon 416 bp exon 8667 bp [gt-ag] intron 1 GenBank accession 135 bp exon 6693 bp [gt-ag] intron 1 GenBank accession 86 RNA-seq supporting reads 4 UHR pooled cells 17 Brain 8 Blood 57 Neuroblastoma (also 8 Primates bodymap) 2 accessions, some from placenta normal (seen once) 132 bp exon 168 bp exon 30636 bp [gt-ag] intron 1 GenBank accession 4 RNA-seq supporting reads 4 Brain (also 2 Primates bodymap) 135 bp exon 26227 bp [gt-ag] intron 52 GenBank accessions 23314 RNA-seq supporting reads 364 UHR pooled cells 10014 Brain 1032 Blood 11566 Neuroblastoma 338 Other (also 18930 Primates bodymap) 184 bp exon 184 bp exon 4009 bp [gt-ag] intron 48 GenBank accessions 30658 RNA-seq supporting reads 452 UHR pooled cells 13136 Brain 1053 Blood 15646 Neuroblastoma 371 Other (also 25027 Primates bodymap) 1 accession from brain capped 5' end, 1 accession 67 bp exon 444 bp exon 444 bp exon 2 accessions, some from normal nasopharynx (seen 2 times) 444 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 2190 bp 585 aa 308 bp 412 bp 2kb including Promoter 174125 bp 1kb
bAug10 1303 bp 355 aa 213 bp 22 bp 2kb including Promoter 140140 bp 1kb
cAug10 1317 bp 322 aa 349 bp 2kb possibly including promoter 95488 bp 1kb
dAug10 952 bp 317 aa 2kb 97341 bp 1kb
eAug10 1174 bp 281 aa 330 bp 36 bp 2kb probably including promoter 85898 bp 1kb
fAug10 703 bp 233 aa 2kb 220558 bp 1kb
gAug10 948 bp 213 aa 151 bp 155 bp 2kb including Promoter 136913 bp 1kb
hAug10 850 bp 175 aa 324 bp 2kb probably including promoter 75270 bp 1kb
iAug10 807 bp 168 aa 302 bp 2kb including Promoter 136891 bp 1kb
jAug10 538 bp 162 aa 52 bp 2kb including Promoter 62305 bp 1kb
kAug10 880 bp 152 aa 420 bp 2kb 166979 bp 1kb
lAug10 1293 bp 148 aa 848 bp 2kb possibly including promoter 61469 bp 1kb
mAug10 547 bp 132 aa 149 bp 2kb including Promoter 30627 bp 1kb
nAug10 433 bp 120 aa 70 bp 2kb 86094 bp 1kb
oAug10 548 bp 109 aa 174 bp 44 bp 2kb including Promoter 151148 bp 1kb
pAug10 572 bp 104 aa 258 bp 57 bp 2kb including Promoter 64415 bp 1kb
qAug10-unspliced 539 bp 100 aa 67 bp 169 bp 2kb possibly including promoter 539 bp 1kb
rAug10 1694 bp 91 aa 1421 bp 51 bp 2kb including Promoter 5757 bp 1kb
sAug10 223 bp 74 aa 2kb 12796 bp 1kb
tAug10 954 bp 72 aa 735 bp 2kb 3307 bp 1kb
uAug10 155 bp 51 aa 2kb 8082 bp 1kb
vaAug10-unspliced 1085 bp 90 aa 198 bp 614 bp 2kb including Promoter 1085 bp 1kb
vbAug10-unspliced 1053 bp 33 aa 950 bp 2kb 1053 bp 1kb
vcAug10-unspliced 947 bp 67 aa 217 bp 526 bp 2kb 947 bp 1kb
vdAug10 683 bp 51 aa 526 bp 2kb 16043 bp 1kb
veAug10-unspliced 674 bp 62 aa 327 bp 158 bp 2kb 674 bp 1kb
vfAug10 575 bp 25 aa 103 bp 394 bp 2kb including Promoter 94119 bp 1kb
vgAug10 554 bp 58 aa 380 bp 2kb including Promoter 61426 bp 1kb
vhAug10-unspliced 506 bp 47 aa 365 bp 2kb 506 bp 1kb
viAug10-unspliced 494 bp 54 aa 329 bp 2kb 494 bp 1kb
vjAug10-unspliced 444 bp 45 aa 304 bp 2kb 444 bp 1kb
vkAug10-unspliced 366 bp 27 aa 282 bp 2kb 366 bp 1kb

Gene neighbors and Navigator on chromosome 10q25 back to top
ABLIM1 Title complex locus ABLIM1, encoding actin binding LIM protein 1. Summary [RefSeq Summary ABLIM1] This gene encodes a cytoskeletal LIM protein that binds to actin filaments via a domain that is homologous to erythrocyte dematin. LIM domains, found in over 60 proteins, play key roles in the regulation of developmental pathways. LIM domains also function as protein-binding interfaces, mediating specific protein-protein interactions. The protein encoded by this gene could mediate such interactions between actin filaments and cytoplasmic targets. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq] Transcribed_gene ABLIM1 Product -----> 37 NewName 10_116528019 NewNameOld dushu klawjybu speejybu GeneId 3983 Other_geneId 3983 LocusLink ABLIM1 Unigene Hs.438236 Hs.538331 Type Spliced_gene Molecular -----> 7 Genetic Locus -----> 8 Pastille_disease Extern KEGG_04360 Details Pathway Axon guidance OMIM_602330 Details OMIM_title actin-binding lim protein family, member 1 Properties ablim lim actin-binding protein 1; limab1 limatin GAD_592780 Details Disease_class NEUROLOGICAL GAD_title Alzheimer Disease GAD_alias Alzheimer's disease Properties [Andrew Grupe , et al. American journal of human genetics 2006 78(1):78-88, CDC] Phs_O14639 Pathway Axon guidance Go_b_iea cytoskeleton organization IEA Expression GO_c_psort nucleus ABLIM1.aAug10 ABLIM1.bAug10 ABLIM1.gAug10 Go_c_iea cytoplasm IEA Regulation Pastille_regulation pastille_regulation_complex_locus pastille_regulation_structure pastille_regulation_uORF Complex_locus Two_product Kozak non_ATG_start Interacts with_gene -----> 14 with_geneId -----> 14 Reference -----> 14 Structure -----> 7 Position Balise Map 10 IntMap 10 116528019 116195042 Cytogenetic 10q25 SMAP S_Parent Genomic_sequence t10_NT_030059.13_113_t10_NT_030059.13_114 Quit Update Attach... Biblio ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               14 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l, .m, .n, .o, .p, .q-u, .r, .s, .t, .u, .va-u, .vb-u, .vc-u, .vd, .ve-u, .vf, .vg, .vh-u, .vi-u, .vj-u, .vk-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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