Human Gene KHSRP (uc002mer.4) Description and Page Index
  Description: Homo sapiens KH-type splicing regulatory protein (KHSRP), mRNA.
RefSeq Summary (NM_003685): The KHSRP gene encodes a multifunctional RNA-binding protein implicated in a variety of cellular processes, including transcription, alternative pre-mRNA splicing, and mRNA localization (Min et al., 1997 [PubMed 9136930]; Gherzi et al., 2004 [PubMed 15175153]).[supplied by OMIM, Apr 2010]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: U94832.1, SRR1163657.113735.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END##
Transcript (Including UTRs)
   Position: hg19 chr19:6,413,119-6,424,822 Size: 11,704 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr19:6,414,123-6,424,712 Size: 10,590 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:6,413,119-6,424,822)mRNA (may differ from genome)Protein (711 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: FUBP2_HUMAN
DESCRIPTION: RecName: Full=Far upstream element-binding protein 2; Short=FUSE-binding protein 2; AltName: Full=KH type-splicing regulatory protein; Short=KSRP; AltName: Full=p75;
FUNCTION: Binds to the dendritic targeting element and may play a role in mRNA trafficking (By similarity). Part of a ternary complex that binds to the downstream control sequence (DCS) of the pre-mRNA. Mediates exon inclusion in transcripts that are subject to tissue-specific alternative splicing. May interact with single- stranded DNA from the far-upstream element (FUSE). May activate gene expression. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'- UTR, possibly by recruiting degradation machinery to ARE- containing mRNAs.
SUBUNIT: Part of a ternary complex containing FUBP2, PTBP1, PTBP2 and HNRPH1. Interacts with PARN.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=A small proportion is also found in the cytoplasm of neuronal cell bodies and dendrites (By similarity).
TISSUE SPECIFICITY: Detected in neural and non-neural cell lines.
DOMAIN: KH domains KH 3 and KH 4 behave as independent binding modules and can interact with different regions of the AU-rich RNA targets of degradation.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
PTM: Phosphorylation at Ser-193 leads to the unfolding of the unstable KH domain 1, creating a site for 14-3-3 YWHAZ binding, which promotes nuclear localization and impairs the RNA degradation function.
SIMILARITY: Belongs to the KHSRP family.
SIMILARITY: Contains 4 KH domains.
SEQUENCE CAUTION: Sequence=AAC50892.1; Type=Frameshift; Positions=304, 309, 466, 473; Sequence=AAH85004.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;

-  MalaCards Disease Associations
  MalaCards Gene Search: KHSRP
Diseases sorted by gene-association score: ataxia, cerebellar, cayman type (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 72.95 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1693.01 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 -42.20110-0.384 Picture PostScript Text
3' UTR -261.211004-0.260 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
IPR015096 - DUF1897
IPR004087 - KH_dom
IPR004088 - KH_dom_type_1

Pfam Domains:
PF00013 - KH domain
PF07650 - KH domain
PF09005 - Domain of unknown function (DUF1897)

SCOP Domains:
54791 - Eukaryotic type KH-domain (KH-domain type I)
54814 - Prokaryotic type KH domain (KH-domain type II)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2HH2
- NMR MuPIT

2HH3
- NMR MuPIT

2JVZ
- NMR MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2OPU - NMR MuPIT 2OPV - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q92945
FrontTopSide
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
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0035925 mRNA 3'-UTR AU-rich region binding

Biological Process:
GO:0000375 RNA splicing, via transesterification reactions
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006397 mRNA processing
GO:0006402 mRNA catabolic process
GO:0008380 RNA splicing
GO:0010586 miRNA metabolic process
GO:0010989 negative regulation of low-density lipoprotein particle clearance
GO:0043488 regulation of mRNA stability
GO:0045019 negative regulation of nitric oxide biosynthetic process
GO:0051028 mRNA transport
GO:0061014 positive regulation of mRNA catabolic process
GO:0061158 3'-UTR-mediated mRNA destabilization
GO:0071345 cellular response to cytokine stimulus
GO:2000628 regulation of miRNA metabolic process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0010494 cytoplasmic stress granule
GO:0016020 membrane
GO:0000178 exosome (RNase complex)


-  Descriptions from all associated GenBank mRNAs
  LF210896 - JP 2014500723-A/18399: Polycomb-Associated Non-Coding RNAs.
U94832 - Human KH type splicing regulatory protein KSRP mRNA, complete cds.
BC085004 - Homo sapiens KH-type splicing regulatory protein, mRNA (cDNA clone MGC:99676 IMAGE:6597976), complete cds.
GQ900928 - Homo sapiens clone HEL-T-40 epididymis secretory sperm binding protein mRNA, complete cds.
U69126 - Human FUSE binding protein 2 (FBP2) mRNA, partial cds.
AK300957 - Homo sapiens cDNA FLJ51330 complete cds, highly similar to Far upstream element-binding protein 2.
MA446473 - JP 2018138019-A/18399: Polycomb-Associated Non-Coding RNAs.
LF341776 - JP 2014500723-A/149279: Polycomb-Associated Non-Coding RNAs.
JD043789 - Sequence 24813 from Patent EP1572962.
LF341777 - JP 2014500723-A/149280: Polycomb-Associated Non-Coding RNAs.
JD389537 - Sequence 370561 from Patent EP1572962.
JD203264 - Sequence 184288 from Patent EP1572962.
LF341778 - JP 2014500723-A/149281: Polycomb-Associated Non-Coding RNAs.
JD359424 - Sequence 340448 from Patent EP1572962.
JD363570 - Sequence 344594 from Patent EP1572962.
JD502680 - Sequence 483704 from Patent EP1572962.
JD341089 - Sequence 322113 from Patent EP1572962.
LF341780 - JP 2014500723-A/149283: Polycomb-Associated Non-Coding RNAs.
JD259322 - Sequence 240346 from Patent EP1572962.
JD544323 - Sequence 525347 from Patent EP1572962.
JD551117 - Sequence 532141 from Patent EP1572962.
LF341788 - JP 2014500723-A/149291: Polycomb-Associated Non-Coding RNAs.
LF341789 - JP 2014500723-A/149292: Polycomb-Associated Non-Coding RNAs.
AB209662 - Homo sapiens mRNA for KH-type splicing regulatory protein (FUSE binding protein 2) variant protein.
HZ409199 - JP 2015528002-A/1796: CHIRAL CONTROL.
HZ460248 - WO 2015190542-A/254: Kit or device and method for detecting biliary tract cancer.
HZ461123 - WO 2015190584-A/620: Kit or device and method for detecting prostate cancer.
HZ461569 - WO 2015190586-A/382: Kit and method for detecting colon cancer.
HZ462166 - WO 2015190591-A/321: Kit and method for detecting breast cancer.
HZ463811 - WO 2015194610-A/247: Kit and method for detecting lung cancer.
HZ464494 - WO 2015194615-A/312: Kit or device and method for detecting hepatic cancer.
HZ465306 - WO 2015194627-A/359: Kit and method for detecting esophageal cancer.
LG052533 - KR 1020150036642-A/1799: CHIRAL CONTROL.
LY495875 - KR 1020170015509-A/254: DETECTION KIT OR DEVICE AND DETECTION METHOD FOR BILIARY TRACT CANCER.
LY496489 - KR 1020170018406-A/359: ESOPHAGEAL CANCER DETECTION KIT OR DEVICE, AND DETECTION METHOD.
LY497212 - KR 1020170016485-A/382: COLORECTAL CANCER DETECTION KIT OR DEVICE, AND DETECTION METHOD.
LY497712 - KR 1020170018409-A/247: KIT OR DEVICE FOR DETECTING LUNG CANCER, AND LUNG CANCER DETECTION METHOD.
LY498395 - KR 1020170018411-A/312: LIVER CANCER DETECTION KIT OR DEVICE, AND DETECTION METHOD.
LY499169 - KR 1020170018412-A/321: BREAST CANCER DETECTION KIT OR DEVICE, AND METHOD FOR DETECTING BREAST CANCER.
LY500996 - KR 1020170016490-A/620: PROSTATE CANCER DETECTION KIT OR DEVICE, AND DETECTION METHOD.
LZ238710 - WO 2017171048-A/371: Kit, device and method for detecting early pancreatic cancer or precancerous lesion of pancreas.
MS869040 - Sequence 254 from Patent EP3156500.
MS869915 - Sequence 620 from Patent EP3156483.
MS880484 - Sequence 321 from Patent EP3156498.
MS884399 - Sequence 382 from Patent EP3156499.
MS994497 - Sequence 359 from Patent EP3159406.
MS996778 - Sequence 247 from Patent EP3159416.
LF341793 - JP 2014500723-A/149296: Polycomb-Associated Non-Coding RNAs.
LF341794 - JP 2014500723-A/149297: Polycomb-Associated Non-Coding RNAs.
BD450071 - Screening method of agents for treating proliferative diseases.
LF341796 - JP 2014500723-A/149299: Polycomb-Associated Non-Coding RNAs.
MA577353 - JP 2018138019-A/149279: Polycomb-Associated Non-Coding RNAs.
MA577354 - JP 2018138019-A/149280: Polycomb-Associated Non-Coding RNAs.
MA577355 - JP 2018138019-A/149281: Polycomb-Associated Non-Coding RNAs.
MA577357 - JP 2018138019-A/149283: Polycomb-Associated Non-Coding RNAs.
MA577365 - JP 2018138019-A/149291: Polycomb-Associated Non-Coding RNAs.
MA577366 - JP 2018138019-A/149292: Polycomb-Associated Non-Coding RNAs.
MA577370 - JP 2018138019-A/149296: Polycomb-Associated Non-Coding RNAs.
MA577371 - JP 2018138019-A/149297: Polycomb-Associated Non-Coding RNAs.
MA577373 - JP 2018138019-A/149299: Polycomb-Associated Non-Coding RNAs.
MA806022 - WO 2018199275-A/282: Kit, device and method for detection of ovary tumor.
MA822739 - WO 2019004436-A/552: Kit, device, and method for detection of lung cancer.
LY616474 - KR 1020180129785-A/371: KIT OR DEVICE FOR DETECTING EARLY STAGE PANCREATIC CANCER OR PANCREATIC CANCER PRECURSOR LESIONS AND DETECTION METHOD THEREFOR.
BC009473 - Homo sapiens, KH-type splicing regulatory protein (FUSE binding protein 2), clone IMAGE:4276204, mRNA.
JD520417 - Sequence 501441 from Patent EP1572962.
JD131786 - Sequence 112810 from Patent EP1572962.
JD406060 - Sequence 387084 from Patent EP1572962.
JD406057 - Sequence 387081 from Patent EP1572962.
JD458511 - Sequence 439535 from Patent EP1572962.
JD458512 - Sequence 439536 from Patent EP1572962.

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

Protein Q92945 (Reactome details) participates in the following event(s):

R-HSA-450499 Protein Kinase B (AKT) phosphorylates KSRP
R-HSA-450592 KSRP binds AU-rich element in 3' UTR of mRNA
R-HSA-451152 MAP kinase p38 phosphorylates KSRP
R-HSA-450422 KSRP recruits RNA degradation activities
R-HSA-450604 KSRP (KHSRP) binds and destabilizes mRNA
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: FUBP2, FUBP2_HUMAN, NM_003685, NP_003676, O00301, Q59EZ9, Q5U4P6, Q92945, Q9UNT5, Q9UQH5
UCSC ID: uc002mer.4
RefSeq Accession: NM_003685
Protein: Q92945 (aka FUBP2_HUMAN or FUB2_HUMAN)
CCDS: CCDS45936.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003685.2
exon count: 20CDS single in 3' UTR: no RNA size: 3262
ORF size: 2136CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4040.00frame shift in genome: no % Coverage: 99.63
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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