Ncbp2 (nuclear cap binding protein subunit 2) - Rat Genome Database

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Gene: Ncbp2 (nuclear cap binding protein subunit 2) Rattus norvegicus
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Symbol: Ncbp2
Name: nuclear cap binding protein subunit 2
RGD ID: 1596188
Description: Enables RNA 7-methylguanosine cap binding activity. Predicted to be involved in several processes, including RNA export from nucleus; mRNA metabolic process; and regulation of primary metabolic process. Part of nuclear cap binding activity complex. Orthologous to several human genes including NCBP2 (nuclear cap binding protein subunit 2); PARTICIPATES IN 5'-end pre-mRNA capping pathway; RNA polymerase II transcription elongation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; fipronil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 20 kDa nuclear cap-binding protein; CBP20; LOC100911481; LOC108348149; LOC689116; NCBP 20 kDa subunit; nuclear cap-binding protein subunit 2; nuclear cap-binding protein subunit 2-like; phosphatidylinositol glycan anchor biosynthesis, class Z; Pigz; similar to nuclear cap binding protein subunit 2
RGD Orthologs
Human
Mouse
Dog
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81182,326,002 - 82,334,839 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1182,322,716 - 82,335,116 (-)EnsemblGRCr8
mRatBN7.21168,821,026 - 68,829,863 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1168,817,740 - 68,851,885 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1177,658,084 - 77,666,921 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01170,320,447 - 70,329,526 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01169,347,167 - 69,356,004 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01172,071,838 - 72,103,087 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1172,921,282 - 72,929,003 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1172,071,839 - 72,080,928 (-)Ensemblrn6Rnor6.0
Rnor_5.01175,147,098 - 75,178,295 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41170,642,907 - 70,651,744 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1168,243,480 - 68,252,317 (-)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)
cytosol  (IEA,ISO)
nuclear cap binding complex  (IBA,IDA,IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO)
RNA cap binding complex  (IEA,ISO)

Molecular Function
DNA binding  (ISO)
mRNA binding  (IEA,ISO,ISS)
nucleic acid binding  (IEA)
protein binding  (ISO)
RNA 7-methylguanosine cap binding  (IDA,IEA,ISO,ISS)
RNA binding  (IEA,ISO)
RNA cap binding  (IBA,IEA)
snRNA binding  (IEA,ISO,ISS)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Cap-binding complex (CBC). Gonatopoulos-Pournatzis T and Cowling VH, Biochem J. 2014 Jan 15;457(2):231-42. doi: 10.1042/BJ20131214.
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. The nuclear cap-binding complex is a novel target of growth factor receptor-coupled signal transduction. Wilson KF, etal., J Biol Chem. 1999 Feb 12;274(7):4166-73.
Additional References at PubMed
PMID:7478990   PMID:7651522   PMID:8601613   PMID:9342333   PMID:11551508   PMID:12434151   PMID:12477932   PMID:15489334   PMID:17873884   PMID:18369367   PMID:18426921   PMID:22658674  
PMID:22673903   PMID:22681889   PMID:23793891   PMID:26382858  


Genomics

Comparative Map Data
Ncbp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81182,326,002 - 82,334,839 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1182,322,716 - 82,335,116 (-)EnsemblGRCr8
mRatBN7.21168,821,026 - 68,829,863 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1168,817,740 - 68,851,885 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1177,658,084 - 77,666,921 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01170,320,447 - 70,329,526 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01169,347,167 - 69,356,004 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01172,071,838 - 72,103,087 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1172,921,282 - 72,929,003 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1172,071,839 - 72,080,928 (-)Ensemblrn6Rnor6.0
Rnor_5.01175,147,098 - 75,178,295 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41170,642,907 - 70,651,744 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1168,243,480 - 68,252,317 (-)NCBICelera
Cytogenetic Map11q22NCBI
NCBP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383196,935,406 - 196,942,528 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3196,935,402 - 196,942,594 (-)Ensemblhg38GRCh38
GRCh373196,662,277 - 196,669,399 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363198,146,670 - 198,153,861 (-)NCBIBuild 36Build 36hg18NCBI36
Build 343198,150,588 - 198,157,710NCBI
Celera3195,248,888 - 195,256,079 (-)NCBICelera
Cytogenetic Map3q29NCBI
HuRef3193,962,416 - 193,969,608 (-)NCBIHuRef
CHM1_13196,633,623 - 196,640,813 (-)NCBICHM1_1
T2T-CHM13v2.03199,661,457 - 199,668,578 (-)NCBIT2T-CHM13v2.0
Ncbp2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391631,767,364 - 31,777,290 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1631,767,331 - 31,780,599 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381631,948,546 - 31,958,472 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1631,948,513 - 31,961,781 (+)Ensemblmm10GRCm38
MGSCv371631,948,632 - 31,958,558 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361631,868,386 - 31,877,928 (+)NCBIMGSCv36mm8
Celera1632,442,367 - 32,452,316 (+)NCBICelera
Cytogenetic Map16B2NCBI
cM Map1622.4NCBI
NCBP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13329,911,457 - 29,943,596 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3329,912,569 - 29,962,175 (-)NCBIcanFam3CanFam3.1
Dog10K_Boxer_Tasha3329,935,367 - 29,967,481 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03330,183,638 - 30,191,656 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
NCBP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13133,178,166 - 133,192,923 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.113133,177,209 - 133,192,935 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213142,870,297 - 142,880,228 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NCBP2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11590,306,640 - 90,314,293 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1590,306,640 - 90,313,019 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604164,083,017 - 64,097,938 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ncbp2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473061,925,831 - 61,931,385 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473061,925,831 - 61,931,451 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ncbp2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1416,770,224 - 16,794,850 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ncbp2
57 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:204
Count of miRNA genes:146
Interacting mature miRNAs:161
Transcripts:ENSRNOT00000002381, ENSRNOT00000071483
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)112252474682951192Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)117330848796070872Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)114644316891443168Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)115892833699753367Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113294306789836615Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117961851999753367Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)117385089499753367Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)115893182292356038Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)115441539196071021Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)115775483796071021Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)116796218499753367Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)117330831599753367Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116859932196497754Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)116985594399753367Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)115107102196071021Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
22 12 73 196 121 116 73 98 73 12 409 216 11 163 90 111 43 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000002381   ⟹   ENSRNOP00000002381
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1182,325,710 - 82,335,116 (-)Ensembl
mRatBN7.2 Ensembl1168,820,734 - 68,829,940 (-)Ensembl
Rnor_6.0 Ensembl1172,071,839 - 72,080,928 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000071483   ⟹   ENSRNOP00000066677
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1182,322,716 - 82,334,839 (-)Ensembl
mRatBN7.2 Ensembl1168,817,740 - 68,829,886 (-)Ensembl
Rnor_6.0 Ensembl1172,921,282 - 72,929,003 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098600   ⟹   ENSRNOP00000084122
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1168,820,734 - 68,851,885 (-)Ensembl
RefSeq Acc Id: NM_001109525   ⟹   NP_001102995
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81182,326,002 - 82,334,839 (-)NCBI
mRatBN7.21168,821,026 - 68,829,863 (-)NCBI
Rnor_6.01172,072,131 - 72,080,968 (-)NCBI
Rnor_5.01175,147,098 - 75,178,295 (-)NCBI
RGSC_v3.41170,642,907 - 70,651,744 (-)RGD
Celera1168,243,480 - 68,252,317 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102995 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61994 (Get FASTA)   NCBI Sequence Viewer  
  B1WC40 (Get FASTA)   NCBI Sequence Viewer  
  EDM11452 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001102995   ⟸   NM_001109525
- UniProtKB: B1WC40 (UniProtKB/Swiss-Prot),   A6IRU9 (UniProtKB/TrEMBL),   A6IRU8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000066677   ⟸   ENSRNOT00000071483
Ensembl Acc Id: ENSRNOP00000002381   ⟸   ENSRNOT00000002381
Ensembl Acc Id: ENSRNOP00000084122   ⟸   ENSRNOT00000098600
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1WC40-F1-model_v2 AlphaFold B1WC40 1-156 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13698219
Promoter ID:EPDNEW_R8742
Type:initiation region
Name:Ncbp2_2
Description:nuclear cap binding protein subunit 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8747  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01172,080,974 - 72,081,034EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596188 AgrOrtholog
BioCyc Gene G2FUF-21075 BioCyc
Ensembl Genes ENSRNOG00000001746 Ensembl
  ENSRNOG00000048589 Ensembl
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:9034150 IMAGE-MGC_LOAD
InterPro NCBP2 UniProtKB/Swiss-Prot
  NCBP2_RRM UniProtKB/Swiss-Prot
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot
  RBD_domain_sf UniProtKB/Swiss-Prot
  RRM_dom UniProtKB/Swiss-Prot
KEGG Report rno:689116 UniProtKB/Swiss-Prot
MGC_CLONE MGC:187828 IMAGE-MGC_LOAD
NCBI Gene 689116 ENTREZGENE
PANTHER NUCLEAR CAP-BINDING PROTEIN SUBUNIT 2 UniProtKB/Swiss-Prot
  PTHR18847 UniProtKB/Swiss-Prot
Pfam RRM_1 UniProtKB/Swiss-Prot
PhenoGen Ncbp2 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000001746 RatGTEx
  ENSRNOG00000048589 RatGTEx
SMART RRM UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot
UniProt A0A8L2Q0F6_RAT UniProtKB/TrEMBL
  A0A8L2QXN2_RAT UniProtKB/TrEMBL
  A6IRU8 ENTREZGENE, UniProtKB/TrEMBL
  A6IRU9 ENTREZGENE, UniProtKB/TrEMBL
  B1WC40 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ncbp2  nuclear cap binding protein subunit 2  LOC108348149  nuclear cap-binding protein subunit 2-like  Data merged from RGD:11474927 737654 PROVISIONAL
2016-08-02 LOC108348149  nuclear cap-binding protein subunit 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2015-07-29 Ncbp2  nuclear cap binding protein subunit 2  LOC100911481  nuclear cap-binding protein subunit 2-like  Data merged from RGD:6492837 737654 PROVISIONAL
2012-10-10 Ncbp2  nuclear cap binding protein subunit 2  Pigz  phosphatidylinositol glycan anchor biosynthesis, class Z  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911481  nuclear cap-binding protein subunit 2-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-04-23 Pigz  phosphatidylinositol glycan anchor biosynthesis, class Z  LOC689116  similar to nuclear cap binding protein subunit 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC689116  similar to nuclear cap binding protein subunit 2      Symbol and Name status set to provisional 70820 PROVISIONAL