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KHDRBS3 KH RNA binding domain containing, signal transduction associated 3 [ Homo sapiens (human) ]

Gene ID: 10656, updated on 3-Apr-2024

Summary

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Official Symbol
KHDRBS3provided by HGNC
Official Full Name
KH RNA binding domain containing, signal transduction associated 3provided by HGNC
Primary source
HGNC:HGNC:18117
See related
Ensembl:ENSG00000131773 MIM:610421; AllianceGenome:HGNC:18117
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
Etle; SALP; SLM2; SLM-2; TSTAR; T-STAR; etoile
Summary
Enables RNA binding activity; identical protein binding activity; and protein domain specific binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome and spermatogenesis. Located in nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis (RPKM 33.1), brain (RPKM 14.0) and 10 other tissues See more
Orthologs
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Genomic context

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See KHDRBS3 in Genome Data Viewer
Location:
8q24.23
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (135457456..135656516)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (136575311..136774451)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (136469699..136659853)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L23a pseudogene 56 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:136271585-136272217 Neighboring gene long intergenic non-protein coding RNA 1591 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:136408400-136409179 Neighboring gene uncharacterized LOC101927872 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:136452424-136453011 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19569 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:136531201-136531857 Neighboring gene MAPRE1 pseudogene 1 Neighboring gene uncharacterized LOC124902046 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:136686601-136686790 Neighboring gene RNA, U1 small nuclear 35, pseudogene

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. SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy. Boeckel JN, et al. Genomics Proteomics Bioinformatics, 2022 Feb. PMID 34273561, Free PMC Article
  2. KHDRBS3 promotes multi-drug resistance and anchorage-independent growth in colorectal cancer. Ukai S, et al. Cancer Sci, 2021 Mar. PMID 33423358, Free PMC Article
  3. Molecular biological analysis of 5-FU-resistant gastric cancer organoids; KHDRBS3 contributes to the attainment of features of cancer stem cell. Ukai S, et al. Oncogene, 2020 Dec. PMID 33046798
  4. [Knock-down of KHDRBS3 gene inhibits proliferation of human ovarian cancer CAOV-3 cells]. Ma X, et al. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi, 2017 Aug. PMID 28871947
  5. Amplification and overexpression of Hsa-miR-30b, Hsa-miR-30d and KHDRBS3 at 8q24.22-q24.23 in medulloblastoma. Lu Y, et al. PLoS One, 2009 Jul 7. PMID 19584924, Free PMC Article

See all (79) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy.
    Title: SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy.
  2. KHDRBS3 promotes paclitaxel resistance and induces glycolysis through modulated MIR17HG/CLDN6 signaling in epithelial ovarian cancer.
    Title: KHDRBS3 promotes paclitaxel resistance and induces glycolysis through modulated MIR17HG/CLDN6 signaling in epithelial ovarian cancer.
  3. KHDRBS3 promotes multi-drug resistance and anchorage-independent growth in colorectal cancer.
    Title: KHDRBS3 promotes multi-drug resistance and anchorage-independent growth in colorectal cancer.
  4. Molecular biological analysis of 5-FU-resistant gastric cancer organoids; KHDRBS3 contributes to the attainment of features of cancer stem cell.
    Title: Molecular biological analysis of 5-FU-resistant gastric cancer organoids; KHDRBS3 contributes to the attainment of features of cancer stem cell.
  5. High KHDRBS3 expression is associated with enhanced stemness in basal-like breast cancer.
    Title: SALL4 - KHDRBS3 network enhances stemness by modulating CD44 splicing in basal-like breast cancer.
  6. Down-regulating the KHDRBS3 gene can cause G0/G1 phase arrest and inhibit cell proliferation in CAOV-3 cells.
    Title: [Knock-down of KHDRBS3 gene inhibits proliferation of human ovarian cancer CAOV-3 cells].
  7. Sam68 and T-STAR could regulate alternative splicing of some pre-mRNAs by bringing two distant UAA motifs into proximity and looping out regions of the pre-mRNA.
    Title: Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68.
  8. Nuclear T-STAR protein expression correlates with HER2 status, hormone receptor negativity and prolonged recurrence free survival in primary breast cancer and decreased cancer cell growth in vitro.
    Title: Nuclear T-STAR protein expression correlates with HER2 status, hormone receptor negativity and prolonged recurrence free survival in primary breast cancer and decreased cancer cell growth in vitro.
  9. SerpinB5 interacts with KHDRBS3 and FBXO32, and KHDRBS3 can interact with FBXO32 mRNA.
    Title: SerpinB5 interacts with KHDRBS3 and FBXO32 in gastric cancer cells.
  10. data implicate hsa-miR-30b, hsa-miR-30d and KHDRBS3 as putative oncogenic target(s) of a novel recurrent medulloblastoma amplicon at 8q24.22-q24.23
    Title: Amplification and overexpression of Hsa-miR-30b, Hsa-miR-30d and KHDRBS3 at 8q24.22-q24.23 in medulloblastoma.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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

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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Replication interactions

Interaction Pubs
Knockdown of KH domain containing, RNA binding, signal transduction associated 3 (KHDRBS3) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev Overexpression of the two GSG family members, SLM1 and SLM2, enhance unspliced HIV RNA cleavage and expression PubMed
Vif vif HIV-1 Vif upregulates the expression of KH domain containing, RNA binding, signal transduction associated 3 (KHDRBS3) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables SH3 domain binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein domain specific binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of alternative mRNA splicing, via spliceosome 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 nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
KH domain-containing, RNA-binding, signal transduction-associated protein 3
Names
KH domain containing, RNA binding, signal transduction associated 3
RNA-binding protein T-Star
Sam68-like phosphotyrosine protein, T-STAR
sam68-like mammalian protein 2

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_006558.3 → NP_006549.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3

    See identical proteins and their annotated locations for NP_006549.1

    Status: VALIDATED

    Source sequence(s)
    AC040914, AF051321, BC032606, BC106028, CB155439
    Consensus CDS
    CCDS6374.1
    UniProtKB/Swiss-Prot
    O75525, Q6NUL8, Q9UPA8
    Related
    ENSP00000348108.5, ENST00000355849.10
    Conserved Domains (3) summary
    pfam16274
    Location:4 → 53
    Qua1; Qua1 domain
    pfam16568
    Location:266 → 320
    Sam68-YY; Tyrosine-rich domain of Sam68
    cd22470
    Location:48 → 160
    KH-I_KHDRBS3; type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    135457456..135656516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047421269.1 → XP_047277225.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X1

  2. XM_005250758.4 → XP_005250815.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X5

    See identical proteins and their annotated locations for XP_005250815.1

    UniProtKB/TrEMBL
    E5RJZ9
    Conserved Domains (3) summary
    pfam16274
    Location:4 → 53
    Qua1; Qua1 domain
    pfam16568
    Location:266 → 296
    Sam68-YY; Tyrosine-rich domain of Sam68
    cd22470
    Location:48 → 160
    KH-I_KHDRBS3; type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins

  3. XM_011516798.2 → XP_011515100.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X4

    UniProtKB/TrEMBL
    E5RJZ9
    Conserved Domains (2) summary
    cd02395
    Location:58 → 177
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16274
    Location:5 → 53
    Qua1; Qua1 domain

  4. XM_011516799.2 → XP_011515101.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X7

    Conserved Domains (2) summary
    cd02395
    Location:58 → 177
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16274
    Location:5 → 53
    Qua1; Qua1 domain

  5. XM_047421268.1 → XP_047277224.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X1

  6. XM_005250757.4 → XP_005250814.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X3

    UniProtKB/TrEMBL
    E5RJZ9
    Conserved Domains (3) summary
    pfam16274
    Location:2 → 25
    Qua1; Qua1 domain
    pfam16568
    Location:238 → 292
    Sam68-YY; Tyrosine-rich domain of Sam68
    cl00098
    Location:20 → 132
    KH-I; K homology (KH) RNA-binding domain, type I

  7. XM_024447052.2 → XP_024302820.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X6

    UniProtKB/TrEMBL
    E5RJZ9
    Related
    ENSP00000431022.1, ENST00000524199.5
    Conserved Domains (3) summary
    cd02395
    Location:30 → 149
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16274
    Location:2 → 25
    Qua1; Qua1 domain
    pfam16568
    Location:238 → 268
    Sam68-YY; Tyrosine-rich domain of Sam68

  8. XM_011516797.3 → XP_011515099.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X2

    See identical proteins and their annotated locations for XP_011515099.1

    UniProtKB/TrEMBL
    E5RJZ9
    Conserved Domains (3) summary
    pfam16274
    Location:1 → 26
    Qua1; Qua1 domain
    pfam16568
    Location:239 → 293
    Sam68-YY; Tyrosine-rich domain of Sam68
    cd22470
    Location:21 → 133
    KH-I_KHDRBS3; type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins

RNA

  1. XR_242372.3 RNA Sequence

  2. XR_001745458.2 RNA Sequence

  3. XR_928287.2 RNA Sequence

  4. XR_001745455.2 RNA Sequence

  5. XR_001745457.2 RNA Sequence

  6. XR_001745456.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    136575311..136774451
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054359589.1 → XP_054215564.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X1

  2. XM_054359593.1 → XP_054215568.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X5

  3. XM_054359592.1 → XP_054215567.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X4

  4. XM_054359595.1 → XP_054215570.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X7

  5. XM_054359591.1 → XP_054215566.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X3

  6. XM_054359594.1 → XP_054215569.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X6

  7. XM_054359590.1 → XP_054215565.1  KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform X2

RNA

  1. XR_008487793.1 RNA Sequence

  2. XR_008487798.1 RNA Sequence

  3. XR_008487797.1 RNA Sequence

  4. XR_008487794.1 RNA Sequence

  5. XR_008487796.1 RNA Sequence

  6. XR_008487795.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75525.1 GenPept UniProtKB/Swiss-Prot:O75525

Gene LinkOut

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