NPAS4 (neuronal PAS domain protein 4) - Rat Genome Database

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Gene: NPAS4 (neuronal PAS domain protein 4) Canis lupus familiaris
Analyze
Symbol: NPAS4
Name: neuronal PAS domain protein 4
RGD ID: 12364000
Description: ENCODES a protein that exhibits protein-containing complex binding (ortholog); INVOLVED IN cellular response to corticosterone stimulus (ortholog); inhibitory postsynaptic potential (ortholog); positive regulation of DNA-templated transcription (ortholog); ASSOCIATED WITH Aicardi-Goutieres Syndrome 3 (ortholog); Bardet-Biedl syndrome (ortholog); congenital muscular dystrophy-dystroglycanopathy type A13 (ortholog); FOUND IN nucleus (inferred); postsynapse (inferred); transcription regulator complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: neuronal PAS domain-containing protein 4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11850,905,614 - 50,912,119 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1850,905,611 - 50,911,086 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1849,514,917 - 49,520,038 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01851,944,546 - 51,949,657 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1851,943,941 - 51,949,559 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11851,045,124 - 51,050,230 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01850,618,773 - 50,623,881 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01851,408,871 - 51,413,979 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
NPAS4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11850,905,614 - 50,912,119 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1850,905,611 - 50,911,086 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1849,514,917 - 49,520,038 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01851,944,546 - 51,949,657 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1851,943,941 - 51,949,559 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11851,045,124 - 51,050,230 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01850,618,773 - 50,623,881 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01851,408,871 - 51,413,979 (-)NCBIUU_Cfam_GSD_1.0
NPAS4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381166,409,158 - 66,426,707 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1166,421,035 - 66,426,707 (+)EnsemblGRCh38hg38GRCh38
GRCh371166,188,475 - 66,194,178 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361165,945,051 - 65,950,753 (+)NCBINCBI36Build 36hg18NCBI36
Build 341165,945,050 - 65,950,753NCBI
Celera1163,508,508 - 63,514,210 (+)NCBICelera
Cytogenetic Map11q13.2NCBI
HuRef1162,516,143 - 62,521,845 (+)NCBIHuRef
CHM1_11166,072,529 - 66,078,231 (+)NCBICHM1_1
T2T-CHM13v2.01166,405,041 - 66,423,054 (+)NCBIT2T-CHM13v2.0
Npas4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39195,034,381 - 5,053,467 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl195,034,383 - 5,040,344 (-)EnsemblGRCm39 Ensembl
GRCm38194,984,353 - 5,003,439 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl194,984,355 - 4,990,316 (-)EnsemblGRCm38mm10GRCm38
MGSCv37194,984,355 - 4,989,971 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36194,984,355 - 4,989,971 (-)NCBIMGSCv36mm8
Celera194,853,421 - 4,859,037 (-)NCBICelera
Cytogenetic Map19ANCBI
cM Map194.2NCBI
Npas4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81211,710,640 - 211,728,038 (-)NCBIGRCr8
mRatBN7.21202,281,260 - 202,298,681 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1202,281,958 - 202,286,724 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1210,634,984 - 210,639,756 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01217,727,377 - 217,732,147 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01210,418,406 - 210,423,176 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01220,260,310 - 220,278,177 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1220,261,008 - 220,265,772 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01227,191,333 - 227,209,087 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41207,597,735 - 207,602,499 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11207,751,187 - 207,755,952 (-)NCBI
Celera1199,821,938 - 199,826,702 (-)NCBICelera
Cytogenetic Map1q43NCBI
Npas4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542218,907,322 - 18,913,428 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542218,907,328 - 18,913,088 (-)NCBIChiLan1.0ChiLan1.0
NPAS4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2967,646,711 - 67,652,386 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11168,689,424 - 68,695,098 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01161,778,329 - 61,784,010 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11165,103,096 - 65,108,825 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1165,103,097 - 65,108,825 (+)Ensemblpanpan1.1panPan2
Npas4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049476,702,444 - 6,718,932 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365993,144,793 - 3,150,377 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365993,144,829 - 3,150,307 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPAS4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl25,990,327 - 5,995,929 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.125,990,936 - 5,995,940 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.225,066,741 - 5,072,489 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NPAS4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.117,856,222 - 7,874,812 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl17,856,939 - 7,862,052 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038105,136,036 - 105,154,282 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Npas4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476719,954,323 - 19,959,360 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476719,953,746 - 19,959,472 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in NPAS4
52 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium
Low 2 6 2 12
Below cutoff 3 4 11 2 4 2 5 4 8 10 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000020162   ⟹   ENSCAFP00000018701
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1850,905,611 - 50,911,086 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000074618   ⟹   ENSCAFP00000044481
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1850,908,861 - 50,911,086 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845024012   ⟹   ENSCAFP00845018858
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1851,943,941 - 51,949,559 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845024027   ⟹   ENSCAFP00845018872
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1851,947,186 - 51,949,559 (-)Ensembl
RefSeq Acc Id: XM_022405627   ⟹   XP_022261335
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11850,905,614 - 50,909,586 (-)NCBI
Dog10K_Boxer_Tasha1849,514,917 - 49,518,286 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038423551   ⟹   XP_038279479
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01851,944,546 - 51,949,657 (-)NCBI
RefSeq Acc Id: XM_038423552   ⟹   XP_038279480
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01851,944,546 - 51,947,905 (-)NCBI
RefSeq Acc Id: XM_038501814   ⟹   XP_038357742
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.11851,045,124 - 51,050,230 (-)NCBI
RefSeq Acc Id: XM_038501815   ⟹   XP_038357743
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.11851,045,124 - 51,048,478 (-)NCBI
RefSeq Acc Id: XM_038562509   ⟹   XP_038418437
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01851,408,871 - 51,413,979 (-)NCBI
RefSeq Acc Id: XM_038562510   ⟹   XP_038418438
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01851,408,871 - 51,412,227 (-)NCBI
RefSeq Acc Id: XM_038626605   ⟹   XP_038482533
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01850,618,773 - 50,623,881 (-)NCBI
RefSeq Acc Id: XM_038626606   ⟹   XP_038482534
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01850,618,773 - 50,622,129 (-)NCBI
RefSeq Acc Id: XM_540832   ⟹   XP_540832
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11850,905,614 - 50,912,119 (-)NCBI
Dog10K_Boxer_Tasha1849,514,917 - 49,520,038 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_540832   ⟸   XM_540832
- Peptide Label: isoform X1
- UniProtKB: A0A8C0YX73 (UniProtKB/TrEMBL),   A0A8C0KP55 (UniProtKB/TrEMBL),   A0A8I3NR20 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_022261335   ⟸   XM_022405627
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSCAFP00000044481   ⟸   ENSCAFT00000074618
RefSeq Acc Id: ENSCAFP00000018701   ⟸   ENSCAFT00000020162
RefSeq Acc Id: XP_038357742   ⟸   XM_038501814
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038357743   ⟸   XM_038501815
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038482533   ⟸   XM_038626605
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038482534   ⟸   XM_038626606
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038279479   ⟸   XM_038423551
- Peptide Label: isoform X1
- UniProtKB: A0A8C0YX73 (UniProtKB/TrEMBL),   A0A8C0KP55 (UniProtKB/TrEMBL),   A0A8I3NR20 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038279480   ⟸   XM_038423552
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038418437   ⟸   XM_038562509
- Peptide Label: isoform X1
- UniProtKB: A0A8C0KP55 (UniProtKB/TrEMBL),   A0A8C0YX73 (UniProtKB/TrEMBL),   A0A8I3NR20 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038418438   ⟸   XM_038562510
- Peptide Label: isoform X2
RefSeq Acc Id: ENSCAFP00845018858   ⟸   ENSCAFT00845024012
RefSeq Acc Id: ENSCAFP00845018872   ⟸   ENSCAFT00845024027
Protein Domains
bHLH   PAS


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000012711 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030017365 UniProtKB/TrEMBL
  ENSCAFG00040012934 UniProtKB/TrEMBL
  ENSCAFG00845013474 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000020162.5 UniProtKB/TrEMBL
  ENSCAFT00000074618.2 UniProtKB/TrEMBL
  ENSCAFT00030032110.1 UniProtKB/TrEMBL
  ENSCAFT00030032151.1 UniProtKB/TrEMBL
  ENSCAFT00040024001.1 UniProtKB/TrEMBL
  ENSCAFT00040024031.1 UniProtKB/TrEMBL
  ENSCAFT00845024012 ENTREZGENE
  ENSCAFT00845024012.1 UniProtKB/TrEMBL
  ENSCAFT00845024027.1 UniProtKB/TrEMBL
Gene3D-CATH PAS domain UniProtKB/TrEMBL
InterPro bHLH_dom UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
  PAS-like_dom_sf UniProtKB/TrEMBL
  PAS_fold_3 UniProtKB/TrEMBL
NCBI Gene NPAS4 ENTREZGENE
PANTHER HYPOXIA-INDUCIBLE FACTOR 1 ALPHA UniProtKB/TrEMBL
  NEURONAL PAS DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
Pfam PAS_3 UniProtKB/TrEMBL
PROSITE BHLH UniProtKB/TrEMBL
  PAS UniProtKB/TrEMBL
SMART PAS UniProtKB/TrEMBL
Superfamily-SCOP SSF55785 UniProtKB/TrEMBL
UniProt A0A8C0KP55 ENTREZGENE
  A0A8C0SFR4_CANLF UniProtKB/TrEMBL
  A0A8C0YX73 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NR20 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NSS6_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:43910 ENTREZGENE