Nipsnap3a (nipsnap homolog 3A (C. elegans)) - Rat Genome Database

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Gene: Nipsnap3a (nipsnap homolog 3A (C. elegans)) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Nipsnap3a
Name: nipsnap homolog 3A (C. elegans)
RGD ID: 1583223
Description: Predicted to be active in mitochondrion. Orthologous to human NIPSNAP3A (nipsnap homolog 3A).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC685080; nipsnap homolog 3A; similar to nipsnap homolog 3A
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8572,409,365 - 72,420,441 (+)NCBIGRCr8
mRatBN7.2567,613,993 - 67,625,067 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl567,614,036 - 67,669,700 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx569,522,182 - 69,532,877 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0571,314,024 - 71,324,723 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0571,311,015 - 71,321,711 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0569,809,492 - 69,820,578 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl569,809,495 - 69,820,312 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0573,973,460 - 73,984,509 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4570,425,039 - 70,435,740 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera566,521,463 - 66,532,164 (+)NCBICelera
Cytogenetic Map5q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Nipsnap3a
49 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:30
Count of miRNA genes:28
Interacting mature miRNAs:29
Transcripts:ENSRNOT00000059828
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53518915368564008Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
1598814Mcs13Mammary carcinoma susceptibility QTL 130.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)56319089069927503Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat


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 endocrine system hemolymphoid system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 7
Low 1
Below cutoff 1 2 3 3 3 2 2 1 3

Sequence


RefSeq Acc Id: ENSRNOT00000059828   ⟹   ENSRNOP00000056573
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl569,809,495 - 69,820,312 (+)Ensembl
RefSeq Acc Id: NM_001161846   ⟹   NP_001155318
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8572,409,425 - 72,420,126 (+)NCBI
mRatBN7.2567,614,036 - 67,624,737 (+)NCBI
Rnor_6.0569,809,535 - 69,820,270 (+)NCBI
Rnor_5.0573,973,460 - 73,984,509 (+)NCBI
RGSC_v3.4570,425,039 - 70,435,740 (+)RGD
Celera566,521,463 - 66,532,164 (+)RGD
Sequence:
RefSeq Acc Id: XR_354019
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8572,409,365 - 72,420,441 (+)NCBI
mRatBN7.2567,613,993 - 67,625,067 (+)NCBI
Rnor_6.0569,809,492 - 69,820,578 (+)NCBI
Rnor_5.0573,973,460 - 73,984,509 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001155318 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000056573
  ENSRNOP00000056573.2
  ENSRNOP00000081717.1
  ENSRNOP00000085534.1
  ENSRNOP00000086152.1
  ENSRNOP00000087647.1
RefSeq Acc Id: NP_001155318   ⟸   NM_001161846
- UniProtKB: D3ZU73 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000056573   ⟸   ENSRNOT00000059828
Protein Domains
NIPSNAP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZU73-F1-model_v2 AlphaFold D3ZU73 1-247 view protein structure

Transcriptome

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

Promoters
RGD ID:13693739
Promoter ID:EPDNEW_R4263
Type:multiple initiation site
Name:Nipsnap3a_1
Description:nipsnap homolog 3A
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_6.0569,809,517 - 69,809,577EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1583223 AgrOrtholog
BioCyc Gene G2FUF-41284 BioCyc
Ensembl Genes ENSRNOG00000010332 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000039113 Ensembl
Ensembl Transcript ENSRNOT00000059828 ENTREZGENE
  ENSRNOT00000059828.4 UniProtKB/TrEMBL
  ENSRNOT00000098020.1 UniProtKB/TrEMBL
  ENSRNOT00000100514.1 UniProtKB/TrEMBL
  ENSRNOT00000107397.1 UniProtKB/TrEMBL
  ENSRNOT00000115539.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.100 UniProtKB/TrEMBL
InterPro Dimeric_a/b-barrel UniProtKB/TrEMBL
  NIPSNAP UniProtKB/TrEMBL
KEGG Report rno:685080 UniProtKB/TrEMBL
NCBI Gene 685080 ENTREZGENE
PANTHER NIPSNAP HOMOLOG 3A UniProtKB/TrEMBL
  NIPSNAP-RELATED UniProtKB/TrEMBL
  PROTEIN NIPSNAP HOMOLOG 3B UniProtKB/TrEMBL
Pfam NIPSNAP UniProtKB/TrEMBL
PhenoGen Nipsnap3a PhenoGen
RatGTEx ENSRNOG00000010332 RatGTEx
  ENSRNOG00000039113 RatGTEx
Superfamily-SCOP Dimer_A_B_barrel UniProtKB/TrEMBL
UniProt A0A8I5ZTD2_RAT UniProtKB/TrEMBL
  A0A8I6A0B7_RAT UniProtKB/TrEMBL
  A0A8I6GG78_RAT UniProtKB/TrEMBL
  D3ZU73 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-01 Nipsnap3a  nipsnap homolog 3A (C. elegans)  LOC685080  similar to nipsnap homolog 3A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC685080  similar to nipsnap homolog 3A      Symbol and Name status set to provisional 70820 PROVISIONAL