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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
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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

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