Nabp2 (nucleic acid binding protein 2) - Rat Genome Database

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Gene: Nabp2 (nucleic acid binding protein 2) Rattus norvegicus
Analyze
Symbol: Nabp2
Name: nucleic acid binding protein 2
RGD ID: 1308158
Description: Predicted to enable DNA polymerase binding activity and G-rich strand telomeric DNA binding activity. Predicted to be involved in several processes, including establishment of protein localization to telomere; mitotic G2/M transition checkpoint; and positive regulation of telomere capping. Predicted to be located in chromosome; cytosol; and nucleoplasm. Predicted to be part of SOSS complex. Orthologous to human NABP2 (nucleic acid binding protein 2); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC362813; MGC125161; nucleic acid-binding protein 2; Obfc2b; oligonucleotide/oligosaccharide-binding fold containing 2B; oligonucleotide/oligosaccharide-binding fold-containing protein 2B; RGD1308158; sensor of single-strand DNA complex subunit B1; sensor of ssDNA subunit B1; similar to RIKEN cDNA 2610036N15; single-stranded DNA-binding protein 1; SOSS complex subunit B1; SOSS-B1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27830,949 - 836,551 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7830,949 - 838,027 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx73,592,698 - 3,598,487 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.075,468,679 - 5,474,468 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.075,766,472 - 5,772,113 (-)NCBIRnor_WKY
Rnor_6.072,820,006 - 2,825,627 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,820,007 - 2,825,608 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,798,470 - 2,805,462 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,693,100 - 1,698,698 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.171,693,101 - 1,700,198 (-)NCBI
Celera7704,441 - 710,047 (-)NCBICelera
Cytogenetic Map7q11NCBI
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
chromosome, telomeric region  (IEA,ISO)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (ISO,ISS)
site of double-strand break  (IEA,ISO)
SOSS complex  (IBA,IEA,ISO,ISS)

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15326124   PMID:18449195   PMID:19605351   PMID:19683501   PMID:23459151   PMID:25589350  


Genomics

Comparative Map Data
Nabp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27830,949 - 836,551 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7830,949 - 838,027 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx73,592,698 - 3,598,487 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.075,468,679 - 5,474,468 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.075,766,472 - 5,772,113 (-)NCBIRnor_WKY
Rnor_6.072,820,006 - 2,825,627 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,820,007 - 2,825,608 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,798,470 - 2,805,462 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,693,100 - 1,698,698 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.171,693,101 - 1,700,198 (-)NCBI
Celera7704,441 - 710,047 (-)NCBICelera
Cytogenetic Map7q11NCBI
NABP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381256,222,015 - 56,229,854 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1256,222,015 - 56,229,854 (+)EnsemblGRCh38hg38GRCh38
GRCh371256,618,126 - 56,623,638 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361254,904,774 - 54,909,795 (+)NCBINCBI36Build 36hg18NCBI36
Celera1256,271,047 - 56,276,531 (+)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1253,657,113 - 53,662,632 (+)NCBIHuRef
CHM1_11256,585,507 - 56,591,029 (+)NCBICHM1_1
T2T-CHM13v2.01256,191,961 - 56,197,479 (+)NCBIT2T-CHM13v2.0
Nabp2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,237,263 - 128,247,426 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10128,237,264 - 128,247,361 (-)EnsemblGRCm39 Ensembl
GRCm3810128,401,394 - 128,411,548 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,401,395 - 128,411,492 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710127,838,451 - 127,846,852 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610127,804,344 - 127,812,745 (-)NCBIMGSCv36mm8
Celera10130,789,654 - 130,798,110 (-)NCBICelera
Cytogenetic Map10D3NCBI
Nabp2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554583,835,205 - 3,840,634 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554583,835,205 - 3,836,841 (+)NCBIChiLan1.0ChiLan1.0
NABP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11232,937,021 - 32,944,754 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1232,937,017 - 32,944,754 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01232,685,521 - 32,693,318 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
NABP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110546,964 - 551,360 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl10546,964 - 551,107 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10610,252 - 614,763 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.010555,475 - 559,986 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl10555,497 - 559,985 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.110532,929 - 537,437 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.010775,919 - 780,430 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.010899,977 - 904,490 (+)NCBIUU_Cfam_GSD_1.0
Nabp2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,231,335 - 58,237,872 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936646632,121 - 639,868 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936646632,390 - 638,900 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NABP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,624,762 - 21,631,706 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,624,654 - 21,631,716 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2523,036,416 - 23,043,271 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NABP2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11152,176,021 - 52,183,204 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1152,177,987 - 52,182,572 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037193,803,203 - 193,810,731 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nabp2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480211,774,237 - 11,780,250 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480211,774,237 - 11,780,822 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nabp2
27 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:282
Count of miRNA genes:188
Interacting mature miRNAs:212
Transcripts:ENSRNOT00000031362
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat

Markers in Region
RH140104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27831,102 - 831,291 (+)MAPPERmRatBN7.2
Rnor_6.072,820,160 - 2,820,348NCBIRnor6.0
Rnor_5.072,798,624 - 2,798,812UniSTSRnor5.0
RGSC_v3.471,693,254 - 1,693,442UniSTSRGSC3.4
Celera7704,595 - 704,783UniSTS
Cytogenetic Map7q11UniSTS


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 5 8 74 35 41 11 5
Low 6 3 3 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000031362   ⟹   ENSRNOP00000036341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7830,949 - 838,027 (-)Ensembl
Rnor_6.0 Ensembl72,820,007 - 2,825,608 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086656   ⟹   ENSRNOP00000074864
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7830,950 - 836,441 (-)Ensembl
Rnor_6.0 Ensembl72,820,007 - 2,825,498 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098497   ⟹   ENSRNOP00000088017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7830,949 - 836,450 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111806   ⟹   ENSRNOP00000090943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7830,952 - 836,499 (-)Ensembl
RefSeq Acc Id: NM_001034939   ⟹   NP_001030111
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27830,949 - 836,441 (-)NCBI
Rnor_6.072,820,006 - 2,825,498 (-)NCBI
Rnor_5.072,798,470 - 2,805,462 (-)NCBI
RGSC_v3.471,693,100 - 1,698,698 (-)RGD
Celera7704,441 - 709,937 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001244819   ⟹   NP_001231748
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27830,949 - 836,551 (-)NCBI
Rnor_6.072,820,006 - 2,825,608 (-)NCBI
Rnor_5.072,798,470 - 2,805,462 (-)NCBI
Celera7704,441 - 710,047 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240769   ⟹   XP_006240831
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27830,949 - 836,542 (-)NCBI
Rnor_6.072,820,006 - 2,825,627 (-)NCBI
Rnor_5.072,798,470 - 2,805,462 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240770   ⟹   XP_006240832
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27830,949 - 836,542 (-)NCBI
Rnor_6.072,820,006 - 2,825,626 (-)NCBI
Rnor_5.072,798,470 - 2,805,462 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240771   ⟹   XP_006240833
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27830,949 - 836,542 (-)NCBI
Rnor_6.072,820,006 - 2,825,627 (-)NCBI
Rnor_5.072,798,470 - 2,805,462 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765029   ⟹   XP_008763251
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27830,949 - 836,448 (-)NCBI
Rnor_6.072,820,006 - 2,825,627 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001030111   ⟸   NM_001034939
- Peptide Label: isoform 1
- UniProtKB: Q3SWT1 (UniProtKB/Swiss-Prot),   A0A0G2K954 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001231748   ⟸   NM_001244819
- Peptide Label: isoform 2
- UniProtKB: Q3SWT1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240833   ⟸   XM_006240771
- Peptide Label: isoform X1
- UniProtKB: Q3SWT1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240831   ⟸   XM_006240769
- Peptide Label: isoform X1
- UniProtKB: Q3SWT1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240832   ⟸   XM_006240770
- Peptide Label: isoform X1
- UniProtKB: Q3SWT1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763251   ⟸   XM_008765029
- Peptide Label: isoform X1
- UniProtKB: Q3SWT1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000036341   ⟸   ENSRNOT00000031362
RefSeq Acc Id: ENSRNOP00000074864   ⟸   ENSRNOT00000086656
RefSeq Acc Id: ENSRNOP00000090943   ⟸   ENSRNOT00000111806
RefSeq Acc Id: ENSRNOP00000088017   ⟸   ENSRNOT00000098497
Protein Domains
OB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3SWT1-F1-model_v2 AlphaFold Q3SWT1 1-211 view protein structure

Transcriptome

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

Promoters
RGD ID:13694936
Promoter ID:EPDNEW_R5461
Type:initiation region
Name:Nabp2_1
Description:nucleic acid binding protein 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.072,825,596 - 2,825,656EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308158 AgrOrtholog
BioCyc Gene G2FUF-35372 BioCyc
Ensembl Genes ENSRNOG00000023480 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036341 ENTREZGENE
  ENSRNOP00000036341.5 UniProtKB/TrEMBL
  ENSRNOP00000074864.2 UniProtKB/TrEMBL
  ENSRNOP00000088017.1 UniProtKB/TrEMBL
  ENSRNOP00000090943 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000031362 ENTREZGENE
  ENSRNOT00000031362.7 UniProtKB/TrEMBL
  ENSRNOT00000086656.2 UniProtKB/TrEMBL
  ENSRNOT00000098497.1 UniProtKB/TrEMBL
  ENSRNOT00000111806 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.50.140 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7319804 IMAGE-MGC_LOAD
InterPro NA-bd_OB-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA-bd_OB_tRNA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:362813 UniProtKB/Swiss-Prot
MGC_CLONE MGC:125161 IMAGE-MGC_LOAD
NCBI Gene 362813 ENTREZGENE
Pfam tRNA_anti-codon UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nabp2 PhenoGen
Superfamily-SCOP SSF50249 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K954 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A9W9_RAT UniProtKB/TrEMBL
  A0A8L2QI91_RAT UniProtKB/TrEMBL
  Q3SWT1 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-05 Nabp2  nucleic acid binding protein 2  Obfc2b  oligonucleotide/oligosaccharide-binding fold containing 2B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Obfc2b  oligonucleotide/oligosaccharide-binding fold containing 2B  RGD1308158  similar to RIKEN cDNA 2610036N15  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1308158  similar to RIKEN cDNA 2610036N15  RGD1308158_predicted  similar to RIKEN cDNA 2610036N15 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1308158_predicted  similar to RIKEN cDNA 2610036N15 (predicted)  LOC362813_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC362813_predicted  similar to RIKEN cDNA 2610036N15 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL