Human Gene PTBP3 (ENST00000374257.6_9) from GENCODE V47lift37
  Description: polypyrimidine tract binding protein 3, transcript variant 7 (from RefSeq NM_001375918.1)
Gencode Transcript: ENST00000374257.6_9
Gencode Gene: ENSG00000119314.16_13
Transcript (Including UTRs)
   Position: hg19 chr9:114,980,715-115,095,899 Size: 115,185 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr9:114,986,131-115,060,145 Size: 74,015 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:114,980,715-115,095,899)mRNA (may differ from genome)Protein (524 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTBP3_HUMAN
DESCRIPTION: RecName: Full=Polypyrimidine tract-binding protein 3; AltName: Full=Regulator of differentiation 1; Short=Rod1;
FUNCTION: RNA-binding protein that mediates pre-mRNA alternative splicing regulation. Plays a role in the regulation of cell proliferation, differentiation and migration. Positive regulator of EPO-dependent erythropoiesis. Participates in cell differentiation regulation by repressing tissue-specific exons. Promotes FAS exon 6 skipping. Binds RNA, preferentially to both poly(G) and poly(U).
SUBUNIT: Interacts with THBS4 (via the acidic amphipathic C- terminus).
TISSUE SPECIFICITY: Expressed in several hematopoietic cell lines examined.
SIMILARITY: Contains 4 RRM (RNA recognition motif) domains.
SEQUENCE CAUTION: Sequence=AAH39896.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAA75466.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BI463123; Type=Frameshift; Positions=92;

-  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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 29.34 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 416.91 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -76.10201-0.379 Picture PostScript Text
3' UTR -1291.405416-0.238 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
IPR006536 - HnRNP-L_PTB
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF11835 - RRM-like domain
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on O95758
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-  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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding

Biological Process:
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0009653 anatomical structure morphogenesis
GO:0030154 cell differentiation
GO:0033119 negative regulation of RNA splicing
GO:0043249 erythrocyte maturation
GO:0045595 regulation of cell differentiation

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  CR749471 - Homo sapiens mRNA; cDNA DKFZp781I1117 (from clone DKFZp781I1117).
BC039896 - Homo sapiens, Similar to ROD1 regulator of differentiation 1 (S. pombe), clone IMAGE:4521078, mRNA, partial cds.
AK001685 - Homo sapiens cDNA FLJ10823 fis, clone NT2RP4001080, highly similar to Regulator of differentiation 1.
BC044585 - Homo sapiens ROD1 regulator of differentiation 1 (S. pombe), mRNA (cDNA clone MGC:57192 IMAGE:5295452), complete cds.
AK302558 - Homo sapiens cDNA FLJ51619 complete cds, highly similar to Regulator of differentiation 1.
KJ902048 - Synthetic construct Homo sapiens clone ccsbBroadEn_11442 PTBP3 gene, encodes complete protein.
CU692212 - Synthetic construct Homo sapiens gateway clone IMAGE:100020899 5' read ROD1 mRNA.
BC045825 - Homo sapiens cDNA clone IMAGE:5262112.
DQ591978 - Homo sapiens piRNA piR-59090, complete sequence.
JA483745 - Sequence 53 from Patent EP2303292.
JD198660 - Sequence 179684 from Patent EP1572962.
JD136060 - Sequence 117084 from Patent EP1572962.
JD427654 - Sequence 408678 from Patent EP1572962.
AB023967 - Homo sapiens mRNA for Rod1, complete cds.
JD353482 - Sequence 334506 from Patent EP1572962.
LF206479 - JP 2014500723-A/13982: Polycomb-Associated Non-Coding RNAs.
MA442056 - JP 2018138019-A/13982: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B1ALY2, B1ALY3, B1ALY5, B1ALY6, B3KME7, ENST00000374257.1, ENST00000374257.2, ENST00000374257.3, ENST00000374257.4, ENST00000374257.5, NM_001375918, O95758, PTBP3_HUMAN, Q68DB9, Q86YB3, Q86YH9, ROD1, uc318lkw.1, uc318lkw.2
UCSC ID: ENST00000374257.6_9
RefSeq Accession: NM_001163788.4
Protein: O95758 (aka PTBP3_HUMAN)

-  Gene Model Information
  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.