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

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Gene: Ncbp2 (nuclear cap binding protein subunit 2) Rattus norvegicus
Analyze
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 positive regulation of mRNA 3'-end processing. 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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81182,326,002 - 82,334,839 (-)NCBIGRCr8
mRatBN7.21168,821,026 - 68,829,863 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1168,817,740 - 68,851,885 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1177,658,084 - 77,666,921 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01170,320,447 - 70,329,526 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01169,347,167 - 69,356,004 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01172,071,838 - 72,103,087 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1172,921,282 - 72,929,003 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1172,071,839 - 72,080,928 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01175,147,098 - 75,178,295 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41170,642,907 - 70,651,744 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1168,243,480 - 68,252,317 (-)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

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

Molecular Function

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 (-)NCBIGRCr8
mRatBN7.21168,821,026 - 68,829,863 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1168,817,740 - 68,851,885 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1177,658,084 - 77,666,921 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01170,320,447 - 70,329,526 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01169,347,167 - 69,356,004 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01172,071,838 - 72,103,087 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1172,921,282 - 72,929,003 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1172,071,839 - 72,080,928 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01175,147,098 - 75,178,295 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41170,642,907 - 70,651,744 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 (-)EnsemblGRCh38hg38GRCh38
GRCh373196,662,277 - 196,669,399 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363198,146,670 - 198,153,861 (-)NCBINCBI36Build 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 Ensembl
GRCm381631,948,546 - 31,958,472 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1631,948,513 - 31,961,781 (+)EnsemblGRCm38mm10GRCm38
MGSCv371631,948,632 - 31,958,558 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)NCBICanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3329,935,367 - 29,967,481 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03330,183,638 - 30,191,656 (-)NCBIROS_Cfam_1.0
NCBP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13133,178,166 - 133,192,923 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473061,925,831 - 61,931,451 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ncbp2
28 total Variants
miRNA Target Status

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 (mRatBN7.2)
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)11169446234Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116611332182169223Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 37 57 41 19 41 2 2 74 35 41 11 2
Low 6 6 9 6
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000002381   ⟹   ENSRNOP00000002381
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1168,820,734 - 68,829,940 (-)Ensembl
Rnor_6.0 Ensembl1172,071,839 - 72,080,928 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000071483   ⟹   ENSRNOP00000066677
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1168,817,740 - 68,829,886 (-)Ensembl
Rnor_6.0 Ensembl1172,921,282 - 72,929,003 (-)Ensembl
RefSeq 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  
Ensembl Protein ENSRNOP00000002381.5
  ENSRNOP00000066677.2
  ENSRNOP00000084122.1
RefSeq Acc Id: NP_001102995   ⟸   NM_001109525
- UniProtKB: B1WC40 (UniProtKB/Swiss-Prot),   A6IRU9 (UniProtKB/TrEMBL),   A6IRU8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066677   ⟸   ENSRNOT00000071483
RefSeq Acc Id: ENSRNOP00000002381   ⟸   ENSRNOT00000002381
RefSeq 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, UniProtKB/TrEMBL
  ENSRNOG00000048589 Ensembl
Ensembl Transcript ENSRNOT00000002381.7 UniProtKB/TrEMBL
  ENSRNOT00000071483.2 UniProtKB/TrEMBL
  ENSRNOT00000098600.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9034150 IMAGE-MGC_LOAD
InterPro GPI_mannosylTrfase UniProtKB/TrEMBL
  NCBP2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NCBP2_RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:689116 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:187828 IMAGE-MGC_LOAD
NCBI Gene 689116 ENTREZGENE
PANTHER NUCLEAR CAP-BINDING PROTEIN SUBUNIT 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR18847 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Glyco_transf_22 UniProtKB/TrEMBL
  RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ncbp2 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001746 RatGTEx
  ENSRNOG00000048589 RatGTEx
SMART RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6GBG9_RAT UniProtKB/TrEMBL
  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