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    SEL1L3 SEL1L family member 3 [ Homo sapiens (human) ]

    Gene ID: 23231, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SEL1L3provided by HGNC
    Official Full Name
    SEL1L family member 3provided by HGNC
    Primary source
    HGNC:HGNC:29108
    See related
    Ensembl:ENSG00000091490 MIM:619914; AllianceGenome:HGNC:29108
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Sel-1L3
    Summary
    Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in lymph node (RPKM 28.3), stomach (RPKM 23.4) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    4p15.2
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (25713964..25863566, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (25696040..25845644, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (25749055..25865188, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S29 pseudogene 11 Neighboring gene SLIRP. pseudogene 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:25726657-25727856 Neighboring gene MT-ND4L pseudogene 22 Neighboring gene MT-CO3 pseudogene 44 Neighboring gene MT-ND4 pseudogene 9 Neighboring gene MT-ND3 pseudogene 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:25796802-25797573 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:25812350-25812914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:25845155-25845923 Neighboring gene Sharpr-MPRA regulatory region 8438 Neighboring gene uncharacterized LOC102723733 Neighboring gene Sharpr-MPRA regulatory region 7924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15327 Neighboring gene uncharacterized LOC124900688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21380 Neighboring gene uncharacterized LOC105374538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:25915129-25915678

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Tissue Proteogenomic Landscape Reveals the Role of Uncharacterized SEL1L3 in Progression and Immunotherapy Response in Lung Adenocarcinoma. Shen CY, et al. J Proteome Res, 2023 Apr 7. PMID 36349894
    2. Association analysis of the chromosome 4p15-p16 candidate region for bipolar disorder and schizophrenia. Christoforou A, et al. Mol Psychiatry, 2007 Nov. PMID 17457313
    3. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. Chalasani N, et al. Gastroenterology, 2010 Nov. PMID 20708005, Free PMC Article
    4. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 1998 Oct 30. PMID 9872452
    5. Differential effects of Tat proteins derived from HIV-1 subtypes B and recombinant CRF02_AG on human brain microvascular endothelial cells: implications for blood-brain barrier dysfunction. Woollard SM, et al. J Cereb Blood Flow Metab, 2014 Jun. PMID 24667918, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SEL1L3 as a link molecular between renal cell carcinoma and atherosclerosis based on bioinformatics analysis and experimental verification.
      Title: SEL1L3 as a link molecular between renal cell carcinoma and atherosclerosis based on bioinformatics analysis and experimental verification.
    2. Tissue Proteogenomic Landscape Reveals the Role of Uncharacterized SEL1L3 in Progression and Immunotherapy Response in Lung Adenocarcinoma.
      Title: Tissue Proteogenomic Landscape Reveals the Role of Uncharacterized SEL1L3 in Progression and Immunotherapy Response in Lung Adenocarcinoma.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Association analysis of the chromosome 4p15-p16 candidate region for bipolar disorder and schizophrenia.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of sel-1 suppressor of lin-12-like 3 (SEL1L3) in primary human brain microvascular endothelial cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21629, FLJ41299, KIAA0746, DKFZp781J1697

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein sel-1 homolog 3
    Names
    sel-1 suppressor of lin-12-like 3
    suppressor of lin-12-like protein 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001297592.2 → NP_001284521.1  protein sel-1 homolog 3 isoform 2

      See identical proteins and their annotated locations for NP_001284521.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding region, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK289687, BC060867, CR749817
      Consensus CDS
      CCDS75113.1
      UniProtKB/Swiss-Prot
      Q68CR1
      Related
      ENSP00000264868.5, ENST00000264868.9
      Conserved Domains (4) summary
      smart00671
      Location:654 → 686
      SEL1; Sel1-like repeats
      COG0790
      Location:572 → 813
      TPR; TPR repeat [Signal transduction mechanisms]
      sd00010
      Location:674 → 704
      SLR; SLR repeat [structural motif]
      pfam08238
      Location:696 → 726
      Sel1; Sel1 repeat

    2. NM_001297594.2 → NP_001284523.1  protein sel-1 homolog 3 isoform 3

      See identical proteins and their annotated locations for NP_001284523.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK289687, BC060867, CR749817
      Consensus CDS
      CCDS77907.1
      Related
      ENSP00000425438.1, ENST00000502949.5
      Conserved Domains (2) summary
      COG0790
      Location:454 → 695
      TPR; TPR repeat [Signal transduction mechanisms]
      sd00010
      Location:556 → 586
      SLR; SLR repeat [structural motif]

    3. NM_015187.5 → NP_056002.2  protein sel-1 homolog 3 isoform 1

      See identical proteins and their annotated locations for NP_056002.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK289687, BC060867, CR749817, DB479874, HY152163
      Consensus CDS
      CCDS47037.1
      UniProtKB/Swiss-Prot
      A0PJH6, A8K0X2, O94847, Q68CR1, Q6P999, Q96G59
      Related
      ENSP00000382767.3, ENST00000399878.8
      Conserved Domains (4) summary
      smart00671
      Location:689 → 721
      SEL1; Sel1-like repeats
      COG0790
      Location:607 → 848
      TPR; TPR repeat [Signal transduction mechanisms]
      sd00010
      Location:709 → 739
      SLR; SLR repeat [structural motif]
      pfam08238
      Location:731 → 761
      Sel1; Sel1 repeat

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      25713964..25863566 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024453953.2 → XP_024309721.1  protein sel-1 homolog 3 isoform X1

      Conserved Domains (2) summary
      COG0790
      Location:454 → 695
      TPR; TPR repeat [Signal transduction mechanisms]
      sd00010
      Location:556 → 586
      SLR; SLR repeat [structural motif]

    2. XM_011513819.3 → XP_011512121.2  protein sel-1 homolog 3 isoform X2

    RNA

    1. XR_007096387.1 RNA Sequence

    2. XR_007096388.1 RNA Sequence

    3. XR_001741182.3 RNA Sequence

    4. XR_007096389.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      25696040..25845644 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054349414.1 → XP_054205389.1  protein sel-1 homolog 3 isoform X1

    2. XM_054349415.1 → XP_054205390.1  protein sel-1 homolog 3 isoform X2

    RNA

    1. XR_008486956.1 RNA Sequence

    2. XR_008486954.1 RNA Sequence

    3. XR_008486955.1 RNA Sequence

    4. XR_008486957.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q68CR1.2 GenPept UniProtKB/Swiss-Prot:Q68CR1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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