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SH3D21 SH3 domain containing 21 [ Homo sapiens (human) ]

Gene ID: 79729, updated on 2-Nov-2024

Summary

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Official Symbol
SH3D21provided by HGNC
Official Full Name
SH3 domain containing 21provided by HGNC
Primary source
HGNC:HGNC:26236
See related
Ensembl:ENSG00000214193 AllianceGenome:HGNC:26236
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
C1orf113
Summary
Predicted to be involved in actin filament organization and cell migration. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in small intestine (RPKM 7.0), skin (RPKM 5.6) and 23 other tissues See more
Orthologs
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Genomic context

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See SH3D21 in Genome Data Viewer
Location:
1p34.3
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (36306368..36330236)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (36168306..36192094)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (36771969..36786948)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 131, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:36680691-36680811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 747 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36689434-36689961 Neighboring gene thyroid hormone receptor associated protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36689962-36690490 Neighboring gene Sharpr-MPRA regulatory regions 10257 and 14041 Neighboring gene ubiquitin conjugating enzyme E2 V2 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 659 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:36726300-36726456 Neighboring gene Sharpr-MPRA regulatory region 2392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36772217-36773017 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36786744-36787628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36788515-36789399 Neighboring gene eva-1 homolog B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36823274-36823774 Neighboring gene serine/threonine kinase 40 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36834695-36835363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36835364-36836031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36837681-36838244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36838245-36838808 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:36839045-36840244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36844393-36844892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 668 Neighboring gene uncharacterized LOC124904012 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:36851839-36853038

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 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. A genome-scale CRISPR/Cas9 knockout screening reveals SH3D21 as a sensitizer for gemcitabine. Masoudi M, et al. Sci Rep, 2019 Dec 16. PMID 31844142, Free PMC Article
  2. Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra. Yu LR, et al. J Proteome Res, 2007 Nov. PMID 17924679
  3. SUMO-specific protease 2 (SENP2) suppresses keratinocyte migration by targeting NDR1 for de-SUMOylation. Xiao N, et al. FASEB J, 2019 Jan. PMID 29969578
  4. POH1 contributes to hyperactivation of TGF-β signaling and facilitates hepatocellular carcinoma metastasis through deubiquitinating TGF-β receptors and caveolin-1. Wang B, et al. EBioMedicine, 2019 Mar. PMID 30745168, Free PMC Article
  5. Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. Benz C, et al. Mol Syst Biol, 2022 Jan. PMID 35044719, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ22938

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in actin filament organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
SH3 domain-containing protein 21
Names
SH3 domain-containing protein C1orf113

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_001162530.2 → NP_001156002.1  SH3 domain-containing protein 21 isoform 1

    See identical proteins and their annotated locations for NP_001156002.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL591845
    UniProtKB/Swiss-Prot
    A4FU49, B4DLI6, D3DPS6, J3KQM5, Q5VTK7, Q86XZ6, Q8N445, Q96DN4, Q9H5W5
    Related
    ENSP00000403476.2, ENST00000453908.8
    Conserved Domains (3) summary
    cd11874
    Location:87 → 139
    SH3_CD2AP-like_2; Second Src Homology 3 domain (SH3B) of CD2-associated protein and similar proteins
    cd12142
    Location:185 → 239
    SH3_D21-like; Src Homology 3 domain of SH3 domain-containing protein 21 (SH3D21) and similar proteins
    cl17036
    Location:2 → 55
    SH3; Src Homology 3 domain superfamily

  2. NM_024676.5 → NP_078952.4  SH3 domain-containing protein 21 isoform 2

    See identical proteins and their annotated locations for NP_078952.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses a downstream start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AL591845
    Consensus CDS
    CCDS30674.2
    UniProtKB/Swiss-Prot
    A4FU49, B4DLI6, D3DPS6, J3KQM5, Q5VTK7, Q86XZ6, Q8N445, Q96DN4, Q9H5W5
    Related
    ENSP00000421294.1, ENST00000505871.7
    Conserved Domains (2) summary
    cd12142
    Location:74 → 128
    SH3_D21-like; Src Homology 3 domain of SH3 domain-containing protein 21 (SH3D21) and similar proteins
    cl17036
    Location:1 → 28
    SH3; Src Homology 3 domain superfamily

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    36306368..36330236
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002340.2 → XP_016857829.1  SH3 domain-containing protein 21 isoform X1

  2. XM_017002341.2 → XP_016857830.1  SH3 domain-containing protein 21 isoform X2

  3. XM_017002344.2 → XP_016857833.1  SH3 domain-containing protein 21 isoform X4

    Conserved Domains (4) summary
    cd11874
    Location:87 → 139
    SH3_CD2AP-like_2; Second Src Homology 3 domain (SH3B) of CD2-associated protein and similar proteins
    cd12142
    Location:185 → 239
    SH3_D21-like; Src Homology 3 domain of SH3 domain-containing protein 21 (SH3D21) and similar proteins
    PHA03247
    Location:239 → 675
    PHA03247; large tegument protein UL36; Provisional
    cl17036
    Location:2 → 55
    SH3; Src Homology 3 domain superfamily

  4. XM_017002345.2 → XP_016857834.1  SH3 domain-containing protein 21 isoform X5

  5. XM_017002342.3 → XP_016857831.1  SH3 domain-containing protein 21 isoform X3

    Conserved Domains (3) summary
    cd11874
    Location:87 → 139
    SH3_CD2AP-like_2; Second Src Homology 3 domain (SH3B) of CD2-associated protein and similar proteins
    cd12142
    Location:185 → 239
    SH3_D21-like; Src Homology 3 domain of SH3 domain-containing protein 21 (SH3D21) and similar proteins
    cl17036
    Location:2 → 55
    SH3; Src Homology 3 domain superfamily

  6. XM_047430650.1 → XP_047286606.1  SH3 domain-containing protein 21 isoform X7

  7. XM_047430644.1 → XP_047286600.1  SH3 domain-containing protein 21 isoform X6

  8. XM_047430651.1 → XP_047286607.1  SH3 domain-containing protein 21 isoform X8

  9. XM_047430653.1 → XP_047286609.1  SH3 domain-containing protein 21 isoform X9

  10. XM_047430654.1 → XP_047286610.1  SH3 domain-containing protein 21 isoform X10

RNA

  1. XR_007063699.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    36168306..36192094
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338756.1 → XP_054194731.1  SH3 domain-containing protein 21 isoform X11

  2. XM_054338753.1 → XP_054194728.1  SH3 domain-containing protein 21 isoform X1

  3. XM_054338754.1 → XP_054194729.1  SH3 domain-containing protein 21 isoform X2

  4. XM_054338755.1 → XP_054194730.1  SH3 domain-containing protein 21 isoform X3

  5. XM_054338757.1 → XP_054194732.1  SH3 domain-containing protein 21 isoform X5

  6. XM_054338759.1 → XP_054194734.1  SH3 domain-containing protein 21 isoform X7

  7. XM_054338758.1 → XP_054194733.1  SH3 domain-containing protein 21 isoform X6

  8. XM_054338760.1 → XP_054194735.1  SH3 domain-containing protein 21 isoform X8

  9. XM_054338761.1 → XP_054194736.1  SH3 domain-containing protein 21 isoform X9

  10. XM_054338762.1 → XP_054194737.1  SH3 domain-containing protein 21 isoform X10

RNA

  1. XR_008486164.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A4FU49.2 GenPept UniProtKB/Swiss-Prot:A4FU49

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