Human Gene HNRNPC (ENST00000553300.6_14) from GENCODE V47lift37
  Description: heterogeneous nuclear ribonucleoprotein C, transcript variant 2 (from RefSeq NM_004500.4)
Gencode Transcript: ENST00000553300.6_14
Gencode Gene: ENSG00000092199.19_20
Transcript (Including UTRs)
   Position: hg19 chr14:21,677,306-21,737,601 Size: 60,296 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr14:21,679,382-21,702,352 Size: 22,971 Coding Exon Count: 7 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:21,677,306-21,737,601)mRNA (may differ from genome)Protein (293 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HNRPC_HUMAN
DESCRIPTION: RecName: Full=Heterogeneous nuclear ribonucleoproteins C1/C2; Short=hnRNP C1/C2;
FUNCTION: Binds pre-mRNA and nucleates the assembly of 40S hnRNP particles. Single HNRNPC tetramers bind 230-240 nucleotides. Trimers of HNRNPC tetramers bind 700 nucleotides. May play a role in the early steps of spliceosome assembly and pre-mRNA splicing. Interacts with poly-U tracts in the 3'-UTR or 5'-UTR of mRNA and modulates the stability and the level of translation of bound mRNA molecules.
SUBUNIT: Tetramer composed of 3 copies of isoform C1 and 1 copy of isoform C2. Assembly of 3 tetramers with bound pre-mRNA gives rise to a 19S complex that interacts with HNRNPA2B1 tetramers. Component of the 40S hnRNP particle. Identified in the spliceosome C complex. Interacts with IGF2BP1.
INTERACTION: Self; NbExp=2; IntAct=EBI-357966, EBI-357966;
SUBCELLULAR LOCATION: Nucleus. Note=Component of ribonucleosomes.
PTM: Phosphorylated on Ser-260 and Ser-299 in resting cells. Phosphorylated on Ser-253 and on 1 serine residue in the poly-Ser stretch at position 238 in response to hydrogen peroxide.
PTM: Sumoylated. Sumoylation reduces affinity for mRNA.
SIMILARITY: Belongs to the RRM HNRPC family. RALY subfamily.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SEQUENCE CAUTION: Sequence=BAD92764.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 116.14 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2215.05 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 -66.20207-0.320 Picture PostScript Text
3' UTR -471.772076-0.227 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
IPR017347 - hnRNP_C_Raly
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

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

SCOP Domains:
48097 - Regulator of G-protein signaling, RGS
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1TXP - NMR MuPIT 1WF2 - NMR MuPIT 3LN4 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P07910
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0005515 protein binding
GO:0008266 poly(U) RNA binding
GO:0031492 nucleosomal DNA binding
GO:0042802 identical protein binding
GO:0070034 telomerase RNA binding
GO:1990247 N6-methyladenosine-containing RNA binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0001649 osteoblast differentiation
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0016070 RNA metabolic process
GO:0032211 negative regulation of telomere maintenance via telomerase
GO:0043044 ATP-dependent chromatin remodeling
GO:0070935 3'-UTR-mediated mRNA stabilization

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005829 cytosol
GO:0015629 actin cytoskeleton
GO:0016020 membrane
GO:0032991 macromolecular complex
GO:0045120 pronucleus
GO:0070062 extracellular exosome
GO:0071013 catalytic step 2 spliceosome
GO:0005697 telomerase holoenzyme complex


-  Descriptions from all associated GenBank mRNAs
  KJ896993 - Synthetic construct Homo sapiens clone ccsbBroadEn_06387 HNRNPC gene, encodes complete protein.
KJ904477 - Synthetic construct Homo sapiens clone ccsbBroadEn_13871 HNRNPC-like gene, encodes complete protein.
KJ905779 - Synthetic construct Homo sapiens clone ccsbBroadEn_15449 HNRNPC gene, encodes complete protein.
KJ905780 - Synthetic construct Homo sapiens clone ccsbBroadEn_15450 HNRNPC gene, encodes complete protein.
AL833432 - Homo sapiens mRNA; cDNA DKFZp313O1739 (from clone DKFZp313O1739).
BC071943 - Homo sapiens cDNA clone IMAGE:3688181, containing frame-shift errors.
AK223517 - Homo sapiens mRNA for Heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNP C1 / hnRNP C2) variant, clone: FCC123A10.
BX247992 - human full-length cDNA clone CS0DG007YK20 of B cells (Ramos cell line) of Homo sapiens (human).
BC003394 - Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA (cDNA clone MGC:5418 IMAGE:3447724), complete cds.
BC066932 - Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA (cDNA clone MGC:87239 IMAGE:4375450), complete cds.
BC103758 - Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA (cDNA clone MGC:117353 IMAGE:6187512), complete cds.
AK126950 - Homo sapiens cDNA FLJ45003 fis, clone BRAWH3011623, highly similar to Heterogeneous nuclear ribonucleoproteins C.
M16342 - Human nuclear ribonucleoprotein particle (hnRNP) C protein mRNA, complete cds.
BC092433 - Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA (cDNA clone IMAGE:30374039), complete cds.
BX247961 - human full-length cDNA clone CS0DA009YK08 of Neuroblastoma of Homo sapiens (human).
AK302213 - Homo sapiens cDNA FLJ53542 complete cds, highly similar to Heterogeneous nuclear ribonucleoproteins C.
JD453250 - Sequence 434274 from Patent EP1572962.
JD048212 - Sequence 29236 from Patent EP1572962.
AK299923 - Homo sapiens cDNA FLJ52975 complete cds, highly similar to Heterogeneous nuclear ribonucleoproteins C.
BC108658 - Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA (cDNA clone MGC:131677 IMAGE:6501821), complete cds.
BC089438 - Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA (cDNA clone MGC:105117 IMAGE:30555817), complete cds.
M29063 - Human hnRNP C2 protein mRNA.
AK225032 - Homo sapiens mRNA for Full-length cDNA clone CS0DI085YM22 of Placenta variant, clone: adKA02528.
BC008364 - Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA (cDNA clone MGC:3150 IMAGE:3354131), complete cds.
BC007052 - Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA (cDNA clone MGC:12469 IMAGE:3686841), complete cds.
BC008423 - Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA (cDNA clone MGC:14574 IMAGE:4102910), complete cds.
AK298906 - Homo sapiens cDNA FLJ54127 complete cds, highly similar to Heterogeneous nuclear ribonucleoproteins C.
AK297482 - Homo sapiens cDNA FLJ52993 complete cds, highly similar to Heterogeneous nuclear ribonucleoprotein C.
BX161480 - human full-length cDNA clone CS0DI085YM22 of Placenta of Homo sapiens (human).
JD504204 - Sequence 485228 from Patent EP1572962.
JD461665 - Sequence 442689 from Patent EP1572962.
AB209527 - Homo sapiens mRNA for Heterogeneous nuclear ribonucleoproteins C1/C2 variant protein.
JD271452 - Sequence 252476 from Patent EP1572962.
JD363804 - Sequence 344828 from Patent EP1572962.
AK292619 - Homo sapiens cDNA FLJ75154 complete cds, highly similar to Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2), mRNA.
JD126556 - Sequence 107580 from Patent EP1572962.
JD390340 - Sequence 371364 from Patent EP1572962.
JD126557 - Sequence 107581 from Patent EP1572962.
JD390341 - Sequence 371365 from Patent EP1572962.
LF345361 - JP 2014500723-A/152864: Polycomb-Associated Non-Coding RNAs.
HQ258021 - Synthetic construct Homo sapiens clone IMAGE:100072330 heterogeneous nuclear ribonucleoprotein C (C1/C2) (HNRNPC), transcript variant 1 (HNRNPC) gene, encodes complete protein.
AB463730 - Synthetic construct DNA, clone: pF1KB4600, Homo sapiens HNRPC gene for Heterogeneous nuclear ribonucleoproteins C1/C2, without stop codon, in Flexi system.
AK312382 - Homo sapiens cDNA, FLJ92712, highly similar to Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2) (HNRPC), transcript variant 1, mRNA.
AK312338 - Homo sapiens cDNA, FLJ92657, highly similar to Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1/C2) (HNRPC), transcript variant 2, mRNA.
JD199371 - Sequence 180395 from Patent EP1572962.
JD036559 - Sequence 17583 from Patent EP1572962.
JD281279 - Sequence 262303 from Patent EP1572962.
JD234902 - Sequence 215926 from Patent EP1572962.
JD026836 - Sequence 7860 from Patent EP1572962.
D28382 - Homo sapiens mRNA for hnRNP C1/C2, 5'UTR region.
JD301143 - Sequence 282167 from Patent EP1572962.
MA580938 - JP 2018138019-A/152864: Polycomb-Associated Non-Coding RNAs.

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

Protein P07910 (Reactome details) participates in the following event(s):

R-HSA-72103 Formation of pre-mRNPs
R-HSA-4570493 RANBP2 (NUP358) SUMOylates HNRNPC with SUMO1
R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-8953854 Metabolism of RNA
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-72172 mRNA Splicing
R-HSA-2990846 SUMOylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: D3DS19, D3DS22, ENST00000553300.1, ENST00000553300.2, ENST00000553300.3, ENST00000553300.4, ENST00000553300.5, HNRPC, HNRPC_HUMAN, NM_004500, P07910, P22628, Q53EX2, Q59FD3, Q5FWE8, Q86SF8, Q86U45, Q96HK7, Q96HM4, Q96IY5, Q9BTS3, uc325ehw.1, uc325ehw.2
UCSC ID: ENST00000553300.6_14
RefSeq Accession: NM_004500.4
Protein: P07910 (aka HNRPC_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.