Nckipsd (NCK interacting protein with SH3 domain) - Rat Genome Database

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Gene: Nckipsd (NCK interacting protein with SH3 domain) Rattus norvegicus
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Symbol: Nckipsd
Name: NCK interacting protein with SH3 domain
RGD ID: 1311323
Description: Predicted to enable Arp2/3 complex binding activity. Involved in regulation of postsynapse assembly. Is active in glutamatergic synapse and postsynapse. Orthologous to human NCKIPSD (NCK interacting protein with SH3 domain); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC301009; NCK-interacting protein with SH3 domain
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
GRCr88118,390,121 - 118,401,121 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8118,390,159 - 118,401,118 (+)EnsemblGRCr8
mRatBN7.28109,511,484 - 109,522,622 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8109,511,658 - 109,522,246 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8115,129,795 - 115,140,088 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08113,328,974 - 113,339,267 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08111,171,772 - 111,182,065 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08117,601,035 - 117,612,302 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8117,600,749 - 117,611,922 (+)Ensemblrn6Rnor6.0
Rnor_5.08116,946,218 - 116,957,203 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48113,863,906 - 113,873,968 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8108,806,304 - 108,816,365 (+)NCBICelera
RGSC_v3.18113,883,284 - 113,893,428 (+)NCBI
Cytogenetic Map8q32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
COP9 signalosome  (IEA,ISO)
glutamatergic synapse  (IDA,IMP)
nucleoplasm  (IEA,ISO)
postsynapse  (IDA,IMP)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. SPIN90 dephosphorylation is required for cofilin-mediated actin depolymerization in NMDA-stimulated hippocampal neurons. Cho IH, etal., Cell Mol Life Sci. 2013 Nov;70(22):4369-83. doi: 10.1007/s00018-013-1391-4. Epub 2013 Jun 14.
2. SPIN90 phosphorylation modulates spine structure and synaptic function. Cho IH, etal., PLoS One. 2013;8(1):e54276. doi: 10.1371/journal.pone.0054276. Epub 2013 Jan 14.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16221862   PMID:16990791   PMID:16999739   PMID:18850735   PMID:21763308  


Genomics

Comparative Map Data
Nckipsd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88118,390,121 - 118,401,121 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8118,390,159 - 118,401,118 (+)EnsemblGRCr8
mRatBN7.28109,511,484 - 109,522,622 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8109,511,658 - 109,522,246 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8115,129,795 - 115,140,088 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08113,328,974 - 113,339,267 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08111,171,772 - 111,182,065 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08117,601,035 - 117,612,302 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8117,600,749 - 117,611,922 (+)Ensemblrn6Rnor6.0
Rnor_5.08116,946,218 - 116,957,203 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48113,863,906 - 113,873,968 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8108,806,304 - 108,816,365 (+)NCBICelera
RGSC_v3.18113,883,284 - 113,893,428 (+)NCBI
Cytogenetic Map8q32NCBI
NCKIPSD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38348,673,844 - 48,685,915 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl348,673,841 - 48,686,364 (-)Ensemblhg38GRCh38
GRCh37348,711,277 - 48,723,348 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36348,686,281 - 48,698,338 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34348,686,283 - 48,698,338NCBI
Celera348,667,186 - 48,679,261 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef348,769,232 - 48,781,781 (-)NCBIHuRef
CHM1_1348,663,370 - 48,675,464 (-)NCBICHM1_1
T2T-CHM13v2.0348,702,805 - 48,714,878 (-)NCBIT2T-CHM13v2.0
Nckipsd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399108,685,515 - 108,696,044 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9108,685,567 - 108,696,043 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm389108,808,346 - 108,818,839 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9108,808,368 - 108,818,844 (+)Ensemblmm10GRCm38
MGSCv379108,710,711 - 108,720,697 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369108,665,603 - 108,675,589 (+)NCBIMGSCv36mm8
Celera9108,415,507 - 108,425,522 (+)NCBICelera
Cytogenetic Map9F2NCBI
cM Map959.63NCBI
Nckipsd
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955532755,997 - 764,855 (-)Ensembl
ChiLan1.0NW_004955532755,997 - 766,202 (-)NCBIChiLan1.0ChiLan1.0
NCKIPSD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2248,639,142 - 48,660,695 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1348,643,302 - 48,665,463 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0348,586,112 - 48,606,811 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1349,676,282 - 49,690,035 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl349,676,282 - 49,688,548 (-)EnsemblpanPan2panpan1.1
NCKIPSD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12040,443,245 - 40,449,859 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2040,442,386 - 40,449,542 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2040,356,437 - 40,367,116 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02040,924,722 - 40,935,400 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2040,925,057 - 40,935,391 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12040,162,226 - 40,172,904 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02040,566,533 - 40,577,212 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02040,848,429 - 40,858,709 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nckipsd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560263,714,481 - 63,724,820 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936529471,913 - 485,389 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936529474,978 - 485,333 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NCKIPSD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1331,363,765 - 31,377,672 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11331,366,574 - 31,377,684 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21334,637,511 - 34,644,922 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NCKIPSD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12210,083,042 - 10,095,654 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2210,081,218 - 10,095,566 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666041156,994,212 - 157,006,851 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nckipsd
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247302,684,762 - 2,695,705 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247302,685,256 - 2,695,387 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Nckipsd
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v18100,139,917 - 100,149,063 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nckipsd
56 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:225
Count of miRNA genes:139
Interacting mature miRNAs:179
Transcripts:ENSRNOT00000047482
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)882352698127352698Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)861019838121662124Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)849849908118871671Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)880768445125768445Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)880768445125768445Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)870041301121080908Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)868690349119799881Rat
10450865Bw175Body weight QTL 1754.1total fat pad mass (VT:0015008)adipose tissue molecular composition measurement (CMO:0000484)884192326129192326Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8103375781129871912Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)855428333127966348Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)885348065130348065Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)898145073122898010Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)880768445125768445Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)880768445125768445Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)891340911131690273Rat


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
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000047482   ⟹   ENSRNOP00000049566
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8118,390,484 - 118,401,118 (+)Ensembl
mRatBN7.2 Ensembl8109,511,658 - 109,522,246 (+)Ensembl
Rnor_6.0 Ensembl8117,600,749 - 117,611,922 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000154226   ⟹   ENSRNOP00000107443
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8118,390,159 - 118,400,158 (+)Ensembl
RefSeq Acc Id: NM_001393927   ⟹   NP_001380856
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88118,390,696 - 118,401,118 (+)NCBI
mRatBN7.28109,512,200 - 109,522,622 (+)NCBI
RefSeq Acc Id: XM_006243754   ⟹   XP_006243816
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88118,390,162 - 118,401,121 (+)NCBI
mRatBN7.28109,511,484 - 109,522,161 (+)NCBI
Rnor_6.08117,601,035 - 117,611,290 (+)NCBI
Rnor_5.08116,946,218 - 116,957,203 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766509   ⟹   XP_008764731
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88118,390,161 - 118,401,121 (+)NCBI
mRatBN7.28109,511,676 - 109,522,161 (+)NCBI
Rnor_6.08117,601,035 - 117,611,290 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039081237   ⟹   XP_038937165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88118,390,665 - 118,396,265 (+)NCBI
mRatBN7.28109,512,165 - 109,517,768 (+)NCBI
RefSeq Acc Id: XM_039081238   ⟹   XP_038937166
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88118,395,011 - 118,401,121 (+)NCBI
mRatBN7.28109,516,512 - 109,522,161 (+)NCBI
RefSeq Acc Id: XM_063265254   ⟹   XP_063121324
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88118,390,121 - 118,401,121 (+)NCBI
RefSeq Acc Id: XP_006243816   ⟸   XM_006243754
- Peptide Label: isoform X2
- UniProtKB: D3ZWX4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764731   ⟸   XM_008766509
- Peptide Label: isoform X2
- UniProtKB: D3ZWX4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000049566   ⟸   ENSRNOT00000047482
RefSeq Acc Id: XP_038937165   ⟸   XM_039081237
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038937166   ⟸   XM_039081238
- Peptide Label: isoform X4
RefSeq Acc Id: NP_001380856   ⟸   NM_001393927
- UniProtKB: D3ZWX4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121324   ⟸   XM_063265254
- Peptide Label: isoform X1
- UniProtKB: D3ZWX4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000107443   ⟸   ENSRNOT00000154226

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZWX4-F1-model_v2 AlphaFold D3ZWX4 1-705 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311323 AgrOrtholog
BioCyc Gene G2FUF-29113 BioCyc
Ensembl Genes ENSRNOG00000031816 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000047482 ENTREZGENE
  ENSRNOT00000047482.7 UniProtKB/TrEMBL
  ENSRNOT00000154226 ENTREZGENE
  ENSRNOT00000154226.1 UniProtKB/TrEMBL
Gene3D-CATH SH3 Domains UniProtKB/TrEMBL
InterPro DUF2013 UniProtKB/TrEMBL
  SH3-like_dom UniProtKB/TrEMBL
  SH3_domain UniProtKB/TrEMBL
  SPIN90/Ldb17 UniProtKB/TrEMBL
NCBI Gene 301009 ENTREZGENE
PANTHER NCK-INTERACTING PROTEIN WITH SH3 DOMAIN UniProtKB/TrEMBL
  PTHR13357 UniProtKB/TrEMBL
Pfam DUF2013 UniProtKB/TrEMBL
  SH3_1 UniProtKB/TrEMBL
PhenoGen Nckipsd PhenoGen
RatGTEx ENSRNOG00000031816 RatGTEx
Superfamily-SCOP SH3 UniProtKB/TrEMBL
UniProt A0ABK0LRT3_RAT UniProtKB/TrEMBL
  D3ZWX4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Nckipsd  NCK interacting protein with SH3 domain   Nckipsd_predicted  NCK interacting protein with SH3 domain (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Nckipsd_predicted  NCK interacting protein with SH3 domain (predicted)      Symbol and Name status set to approved 70820 APPROVED