Homo sapiens gene C9orf16, encoding chromosome 9 open reading frame 16.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), 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 4 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 1.7 times the average gene in this release. The sequence of this gene is defined by 189 GenBank accessions from 173 cDNA clones, some from brain (seen 22 times), eye (12), t-lymphocytes (12), lung (9), hypothalamus (6), skin (6), uterus (6) and 86 other tissues. We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 5 distinct gt-ag introns. Transcription produces 5 different mRNAs, 4 alternatively spliced variants and 1 unspliced form. There are 5 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by presence or absence of 3 cassette exons, overlapping exons with different boundaries.
Function: There is one article specifically referring to this gene in PubMed. A putative protein interactor has been described (KRT20ANDKRT12).
Protein coding potential: The spliced and the unspliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 COOH complete), apparently mammals specific. The remaining 3 mRNA variants (3 spliced; 1 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by 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 9, links to other databases and other names
Map: This gene C9orf16 maps on chromosome 9, at 9q34.1 according to Entrez Gene. In AceView, it covers 3.74 kb, from 130922473 to 130926211 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 79095, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as C9orf16, EST00098, MGC4639 or FLJ12823, LOC79095. It has been described as hypothetical protein LOC79095.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene 1110008P14Rik (e=5 10-19)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
C9orf16 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 0.14 4.10 1.45 1.35 1.45 0.29 8.78 2.35 4.39 1.26 3.82 10.8 5.79 4.10 5.79 2.90 4.39 7.64 4.39 5.04 10.8 8.78 1.10 2.52 1.35 3.57 3.10 2.90 3.10 6.65 4.39 3.33 1.10 0.39 2.35 4.10 1.35 1.18 1.66 4.71 3.57 18.8 2.70 0.72 1.18 0.63 5.40 5.79 1.91 2.52 10.1 2.52 2.52 3.57 1.35 0.89 3.57 4.71 2.52 1.45 9.41 0.96 4.39 2.19 1.18 1.35 20.2 16.4 2.52 3.10 1.66 1.10 0.32 5.79 5.04 6.65 3.82 2.35 11.6 2.70 1.91 0.48 5.40 7.64 10.1 4.71 3.57 2.05 1.45 10.8 8.78 1.91 0.22 1.26 0.34 1.35 4.39 0.21 3.33 3.33 3.82 7.64 4.71 8.19 2.70 10.8 8.78 11.6 9.41 8.19 6.21 2.19 1.78 3.57 6.65 1.02 0.18 2.35 4.39 2.52 1.91 3.57 1.10 15.3 2.70 4.10 2.35 0.68 10.1 5.79 3.82 5.40 2.35 5.40 10.8 5.40 4.71 5.04 5.79 5.40 6.65 0.14 0.72 0.18 1.18 0.07 1.45 1.35 0.36 0.36 0.72 4.71 7.13 5.40 11.6 2.52 2.35 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!.
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          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 C9orf16 5' 3' encoded on plus strand of chromosome 9 from 130,922,473 to 130,926,211 163313 a [NM] b-u 3503 3470 c 3503 158 d 3503 1048 e 500bp 0 293 bp exon 293 bp exon 2956 bp [gt-ag] intron 110 GenBank accessions 163203 RNA-seq supporting reads 22696 UHR pooled cells 31655 Brain 8452 Blood 99789 Neuroblastoma 611 Other (also 6223 Primates bodymap) 486 bp exon 146 accessions, NM_024112.3 some from brain (seen 16 times) t-lymphocytes (12), eye (9) lung (7), hypothalamus (6) Validated 3' end, 44 accessions 486 bp exon 3618 bp exon 3618 bp exon 210 bp uORF 3618 bp exon 3618 bp exon 16 accessions, some from testis (seen 3 times) brain (2), cerebellum (2) embryonal carcinoma, cell line (2) 2 pooled wilms' tumors one primary and onemetastatic to brain (once) capped 5' end, 7 accessions Validated 3' end, 1 accession Validated 3' end, 2 accessions 3618 bp exon 179 bp exon 1517 bp [gt-ag] intron 9 GenBank accessions 3494 RNA-seq supporting reads 703 UHR pooled cells 276 Brain 92 Blood 2417 Neuroblastoma 6 Other (also 115 Primates bodymap) 949 bp exon 949 bp exon 490 bp [gt-ag] intron 7 GenBank accessions 3463 RNA-seq supporting reads 695 UHR pooled cells 300 Brain 109 Blood 2354 Neuroblastoma 5 Other (also 7 Primates bodymap) 482 bp exon 15 accessions, some from brain (seen 3 times) neuroblastoma cot 25-normalized (2) subthalamic nucleus (2) cerebellum (once), duodenal adenocarcinoma cell line (once) 482 bp exon 128 bp exon 128 bp exon 1517 bp [gt-ag] intron 9 GenBank accessions 3494 RNA-seq supporting reads 703 UHR pooled cells 276 Brain 92 Blood 2417 Neuroblastoma 6 Other (also 115 Primates bodymap) 341 bp exon 341 bp exon 1098 bp [gt-ag] intron 2 GenBank accessions 156 RNA-seq supporting reads 52 UHR pooled cells 14 Brain 7 Blood 83 Neuroblastoma 2 accessions, some from eye (seen 2 times) cornea (once), lens (once) Validated 3' end, 1 accession 481 bp exon 26 bp exon 1517 bp [gt-ag] intron 9 GenBank accessions 3494 RNA-seq supporting reads 703 UHR pooled cells 276 Brain 92 Blood 2417 Neuroblastoma 6 Other (also 115 Primates bodymap) 112 bp exon 1327 bp [gt-ag] intron 1 GenBank accession 1047 RNA-seq supporting reads 204 UHR pooled cells 73 Brain 35 Blood 735 Neuroblastoma (also 2 Primates bodymap) 484 bp exon 484 bp exon 1 accession from eye from optic nerve Validated 3' end, 1 accession 484 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 779 bp 180 aa 234 bp 2kb 3735 bp 1kb
bAug10-unspliced 3618 bp 145 aa 158 bp 3022 bp 207 bp 2kb including Promoter 3618 bp 1kb
cAug10 1610 bp 89 aa 1110 bp 230 bp 2kb probably including promoter 3617 bp 1kb
dAug10 950 bp 58 aa 771 bp 2kb probably including promoter 3565 bp 1kb
eAug10 622 bp 83 aa 341 bp 29 bp 2kb 3466 bp 1kb

Gene neighbors and Navigator on chromosome 9q34.1 back to top
C9orf117 C R TTC16 C R P CDK9 D C I R P FPGS D C R P R R C R SLC25A25 C R P C G R LCN2 D C I R P C9orf16 I R P DNM1 D C I R P C9orf119 C R R R COQ4andSLC27A4 D C I R P URM1 C I R P CERCAM C R P G ODF2 C I R P GLE1 D C I R P SPTAN1 D C I R P TMSL4 C R P PTRH1 C R C R P TOR2A C I R P SH2D3C D C I R P ENG D C I R P ST6GALNAC6andAK1 C R P ST6GALNAC4 C I R P PIP5KL1 C I R P DPM2 C R P FAM102A D C R P NAIF1 R G R D C I R P PTGES2 D C I R P CIZ1 D C I R P GOLGA2 D P MIR199B C C R P TRUB2 C R R C 100kb 0 STXBP1, 280 accessions 15 variants C9orf117, 43 accessions 8 variants TTC16, 62 accessions, 9 variants CDK9, 236 accessions, 5 variants FPGS, 354 accessions, 20 variants wyler, 27 accessions, 2 variants kutera, 12 accessions 4 variants meetabu, 1 accession satabu, 54 accessions 3 variants SLC25A25, 247 accessions 11 variants kleeplabu, 18 accessions LOC389791, 10 accessions LCN2, 392 accessions, 10 variants C9orf16, 182 accessions 5 variants DNM1, 405 accessions, 20 variants C9orf119, 121 accessions 9 variants kleetawbo, 7 accessions 3 variants zawswee, 4 accessions COQ4andSLC27A4, 527 accessions 22 variants URM1, 507 accessions, 10 variants CERCAM, 589 accessions 20 variants LOC100129352, 1 accession ODF2, 586 accessions, 54 variants GLE1, 381 accessions, 11 variants SPTAN1, 493 accessions 25 variants fleetyby, 2 accessions fleytyby, 1 accession flortyby, 1 accession floytyby, 1 accession glatyby, 2 accessions glytyby, 1 accession rupleybu, 1 accession jorswee, 1 accession snervoby, 3 accessions gleytyby, 1 accession martabu, 1 accession rekoro, 1 accession monoybu, 2 accessions hohamu, 2 accessions, 2 variants meeswee, 2 accessions noswee, 1 accession rerpleybu, 2 accessions skorsyby, 11 accessions skawtawbo, 7 accessions klawtyby, 1 accession kleetyby, 5 accessions rokoro, 1 accession rorpleybu, 1 accession sypleybu, 1 accession partabu, 1 accession tusher, 1 accession sherteebo, 1 accession puswee, 1 accession parswee, 1 accession sawpleybu, 1 accession reyswee, 1 accession sotabu, 2 accessions royswee, 1 accession sawtabu, 1 accession tatabu, 1 accession pleytyby, 1 accession plortyby, 1 accession seypleybu, 1 accession totabu, 1 accession skutyby, 1 accession skertyby, 2 accessions skortyby, 1 accession tapleybu, 1 accession slutyby, 11 accessions slartyby, 2 accessions koyvarby, 2 accessions slawtyby, 5 accessions sleytyby, 2 accessions mito_carr.18, 1 accession teyswee, 1 accession vertabu, 1 accession smotyby, 2 accessions voytabu, 1 accession smawtyby, 1 accession snatyby, 1 accession snutyby, 1 accession snotyby, 1 accession snawtyby, 1 accession rawvarby, 6 accessions vyvarby, 3 accessions teypleybu, 1 accession warswee, 1 accession snortyby, 1 accession spytyby, 2 accessions sputyby, 1 accession werswee, 1 accession spotyby, 1 accession spartyby, 2 accessions watora, 2 accessions spawtyby, 1 accession speetyby, 2 accessions TMSL4, 9 accessions woytabu, 1 accession spertyby, 2 accessions speytyby, 1 accession spoytyby, 1 accession statyby, 4 accessions blawvarby, 3 accessions stotyby, 1 accession sharswee, 1 accession chotabu, 1 accession steetyby, 1 accession shawswee, 1 accession stortyby, 1 accession varpleybu, 13 accessions sherswee, 1 accession stoytyby, 1 accession chertabu, 1 accession swutyby, 1 accession chortabu, 1 accession sweetyby, 2 accessions swertyby, 1 accession sweytyby, 2 accessions swortyby, 1 accession swoytyby, 1 accession batuby, 2 accessions, 2 variants bytuby, 2 accessions butuby, 3 accessions blyswee, 1 accession glawvarby, 2 accessions wypleybu, 1 accession bawtuby, 1 accession bertuby, 1 accession blutabu, 1 accession blotabu, 1 accession bortuby, 1 accession blartabu, 1 accession boytuby, 1 accession bluteebo, 2 accessions wopleybu, 1 accession shareyby, 2 accessions dartuby, 2 accessions dertuby, 1 accession deytuby, 1 accession dortuby, 1 accession doytuby, 1 accession flertyby, 1 accession glutyby, 1 accession lortabu, 1 accession loytabu, 1 accession kuswee, 2 accessions rikoro, 2 accessions gloytyby, 1 accession rukoro, 1 accession klutyby, 5 accessions shawteebo, 1 accession rawpleybu, 1 accession mawtabu, 2 accessions reepleybu, 1 accession waler, 2 accessions paswee, 1 accession beyvarby, 2 accessions notabu, 1 accession nortabu, 1 accession borvarby, 1 accession pawtabu, 1 accession klortyby, 5 accessions platyby, 1 accession plytyby, 1 accession plutyby, 3 accessions neygar, 2 accessions sarpleybu, 1 accession reeswee, 1 accession roytabu, 3 accessions plertyby, 1 accession serpleybu, 2 accessions ploytyby, 1 accession skatyby, 2 accessions skytyby, 1 accession votabu, 1 accession juvarby, 6 accessions skartyby, 1 accession skeetyby, 2 accessions vartabu, 1 accession skeytyby, 1 accession vawtabu, 1 accession skoytyby, 1 accession kuvarby, 7 accessions weeler, 1 accession slytyby, 2 accessions slotyby, 1 accession slertyby, 1 accession slortyby, 2 accessions sarswee, 1 accession veetabu, 1 accession soyswee, 1 accession tupleybu, 2 accessions smytyby, 1 accession yukoro, 1 accession smeetyby, 1 accession smertyby, 1 accession snytyby, 5 accessions wytabu, 1 accession toysher, 1 accession waswee, 1 accession klerplabu, 6 accessions spatyby, 1 accession weytabu, 1 accession zarswee, 1 accession vypleybu, 3 accessions vupleybu, 1 accession shyswee, 3 accessions zatabu, 1 accession sportyby, 2 accessions shoyteebo, 10 accessions shoyvarby, 1 accession startyby, 1 accession chaler, 7 accessions stawtyby, 2 accessions chytabu, 1 accession stertyby, 2 accessions vawpleybu, 1 accession cheetabu, 1 accession blyteebo, 1 accession swotyby, 2 accessions sheyswee, 1 accession swawtyby, 1 accession verpleybu, 2 accessions wapleybu, 1 accession shatabu, 6 accessions flyswee, 1 accession beetuby, 1 accession beytuby, 2 accessions datuby, 1 accession florswee, 1 accession dutuby, 1 accession deetuby, 1 accession gloswee, 1 accession blertabu, 1 accession glorswee, 1 accession kluswee, 1 accession weepleybu, 1 accession yokoro, 2 accessions PTRH1, 141 accessions 12 variants glawtyby, 2 accessions vawler, 4 accessions TOR2A, 183 accessions 10 variants SH2D3C, 426 accessions 27 variants ENG, 464 accessions, 16 variants ST6GALNAC6andAK1, 690 accessions 30 variants ST6GALNAC4, 256 accessions 4 variants PIP5KL1, 45 accessions 15 variants DPM2, 328 accessions, 6 variants FAM102A, 266 accessions 10 variants NAIF1, 146 accessions 7 variants peygar, 3 accessions LOC100289019, 33 accessions 5 variants PTGES2, 476 accessions 18 variants CIZ1, 536 accessions, 26 variants GOLGA2, 338 accessions 14 variants MIR199B, 2 accessions slusyby, 27 accessions TRUB2, 323 accessions 8 variants cheeswee, 1 accession chuler, 1 accession choler, 30 accessions 4 variants warpleybu, 1 accession WDR34, 283 accessions 13 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               1 article in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b-u, .c, .d, .e Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes I

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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