Human Gene KHDRBS2 (ENST00000281156.5) from GENCODE V44
  Description: Homo sapiens KH RNA binding domain containing, signal transduction associated 2 (KHDRBS2), transcript variant 2, mRNA. (from RefSeq NM_152688)
Gencode Transcript: ENST00000281156.5
Gencode Gene: ENSG00000112232.10
Transcript (Including UTRs)
   Position: hg38 chr6:61,679,961-62,286,225 Size: 606,265 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg38 chr6:61,680,963-62,285,948 Size: 604,986 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr6:61,679,961-62,286,225)mRNA (may differ from genome)Protein (349 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=KH domain-containing, RNA-binding, signal transduction-associated protein 2; AltName: Full=Sam68-like mammalian protein 1; Short=SLM-1; Short=hSLM-1;
FUNCTION: RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. Its phosphorylation by FYN inhibits its ability to regulate splice site selection. Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich exonic enhancer. May function as an adapter protein for Src kinases during mitosis. Binds both poly(A) and poly(U) homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability (By similarity).
SUBUNIT: Self-associates to form homooligomers. Interacts with SAFB, SFRS9 and YTHDC1. Found in a complex with KHDRBS1, KHDRBS2 and KHDRBS3. Interacts with the SH3 domains of FYN and PLCG1. Interacts with the SH2 domains of FYN, GRAP2, PLCG1 and RASA1 (By similarity). Interacts with RBMX.
INTERACTION: P38159:RBMX; NbExp=2; IntAct=EBI-742808, EBI-743526;
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Highly expressed in brain, lung, kidney and small intestine. Weakly expressed in placenta, liver, spleen, thymus, ovary and colon.
PTM: Methylated.
PTM: Tyrosine phosphorylated by FYN, PTK6 and SRC. Tyrosine phosphorylated by SRC during mitosis (By similarity).
SIMILARITY: Belongs to the KHDRBS family.
SIMILARITY: Contains 1 KH domain.

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.91 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 32.15 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -134.30277-0.485 Picture PostScript Text
3' UTR -197.401002-0.197 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004087 - KH_dom
IPR004088 - KH_dom_type_1

Pfam Domains:
PF00013 - KH domain

ModBase Predicted Comparative 3D Structure on Q5VWX1
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008143 poly(A) binding
GO:0008266 poly(U) RNA binding
GO:0017124 SH3 domain binding
GO:0042169 SH2 domain binding
GO:0042802 identical protein binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006397 mRNA processing
GO:0048024 regulation of mRNA splicing, via spliceosome

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm

-  Descriptions from all associated GenBank mRNAs
  BC034043 - Homo sapiens KH domain containing, RNA binding, signal transduction associated 2, mRNA (cDNA clone MGC:26664 IMAGE:4796658), complete cds.
AY077838 - Homo sapiens Sam68-like mammalian protein 1 (SLM1) mRNA, complete cds.
AK292043 - Homo sapiens cDNA FLJ77356 complete cds, highly similar to Homo sapiens KH domain containing, RNA binding, signal transduction associated 2 (KHDRBS2), mRNA.
HQ447866 - Synthetic construct Homo sapiens clone IMAGE:100071215; CCSB001138_02 KH domain containing, RNA binding, signal transduction associated 2 (KHDRBS2) gene, encodes complete protein.
KJ900431 - Synthetic construct Homo sapiens clone ccsbBroadEn_09825 KHDRBS2 gene, encodes complete protein.
CU689822 - Synthetic construct Homo sapiens gateway clone IMAGE:100019052 5' read KHDRBS2 mRNA.
AK095983 - Homo sapiens cDNA FLJ38664 fis, clone HLUNG2002334, highly similar to Homo sapiens KH domain containing, RNA binding, signal transduction associated 2 (KHDRBS2), mRNA.
JD305736 - Sequence 286760 from Patent EP1572962.
JD043592 - Sequence 24616 from Patent EP1572962.
JD245255 - Sequence 226279 from Patent EP1572962.
JD300202 - Sequence 281226 from Patent EP1572962.
JD300670 - Sequence 281694 from Patent EP1572962.
JD533774 - Sequence 514798 from Patent EP1572962.
JD141253 - Sequence 122277 from Patent EP1572962.
JD157221 - Sequence 138245 from Patent EP1572962.
JD462283 - Sequence 443307 from Patent EP1572962.
JD173608 - Sequence 154632 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q5VWX1 (Reactome details) participates in the following event(s):

R-HSA-8849032 PTK6 phosphorylates KHDRBS2
R-HSA-8849468 PTK6 Regulates Proteins Involved in RNA Processing
R-HSA-8848021 Signaling by PTK6
R-HSA-9006927 Signaling by Non-Receptor Tyrosine Kinases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: A8K7M8, ENST00000281156.1, ENST00000281156.2, ENST00000281156.3, ENST00000281156.4, KHDR2_HUMAN, NM_152688, Q5VWX1, Q8N4I4, Q8TCZ4, SLM1, uc003peg.1, uc003peg.2, uc003peg.3, uc003peg.4
UCSC ID: ENST00000281156.5
RefSeq Accession: NM_152688
Protein: Q5VWX1 (aka KHDR2_HUMAN)
CCDS: CCDS4963.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.