NPHP4 (nephrocystin 4) - Rat Genome Database

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Gene: NPHP4 (nephrocystin 4) Sus scrofa
Analyze
Symbol: NPHP4
Name: nephrocystin 4
RGD ID: 13852919
Description: INVOLVED IN flagellated sperm motility (ortholog); photoreceptor cell maintenance (ortholog); photoreceptor cell outer segment organization (ortholog); ASSOCIATED WITH atypical hemolytic-uremic syndrome (ortholog); Bardet-Biedl syndrome (ortholog); CAKUT (ortholog); FOUND IN ciliary basal body (ortholog); INTERACTS WITH deoxynivalenol
Type: ncrna (Ensembl: protein-coding)
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl666,815,281 - 66,928,146 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1666,815,282 - 66,928,245 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2661,821,151 - 61,829,018 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Genomics

Comparative Map Data
NPHP4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl666,815,281 - 66,928,146 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1666,815,282 - 66,928,245 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2661,821,151 - 61,829,018 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NPHP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3815,862,811 - 5,992,425 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl15,862,811 - 5,992,473 (-)EnsemblGRCh38hg38GRCh38
GRCh3715,922,871 - 6,052,485 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3615,845,457 - 5,975,118 (-)NCBINCBI36Build 36hg18NCBI36
Build 3415,857,135 - 5,986,797NCBI
Celera15,037,702 - 5,167,377 (-)NCBICelera
Cytogenetic Map1p36.31NCBI
HuRef15,071,502 - 5,201,940 (-)NCBIHuRef
CHM1_115,911,568 - 6,041,216 (-)NCBICHM1_1
T2T-CHM13v2.015,387,041 - 5,518,608 (-)NCBIT2T-CHM13v2.0
Nphp4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394152,561,163 - 152,647,641 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4152,561,163 - 152,647,640 (+)EnsemblGRCm39 Ensembl
GRCm384152,476,706 - 152,563,184 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4152,476,706 - 152,563,183 (+)EnsemblGRCm38mm10GRCm38
MGSCv374151,852,251 - 151,937,293 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364151,321,942 - 151,406,934 (+)NCBIMGSCv36mm8
Celera4154,764,281 - 154,849,333 (+)NCBICelera
Cytogenetic Map4E2NCBI
cM Map483.14NCBI
Nphp4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85168,270,522 - 168,356,393 (+)NCBIGRCr8
mRatBN7.25162,986,157 - 163,073,708 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5162,988,370 - 163,073,706 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5165,691,473 - 165,776,590 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05167,513,074 - 167,598,197 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05167,475,281 - 167,560,405 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05169,647,581 - 169,744,662 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5169,659,188 - 169,744,660 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05173,201,362 - 173,298,422 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45169,711,038 - 169,797,486 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5161,218,067 - 161,302,859 (+)NCBICelera
Cytogenetic Map5q36NCBI
Nphp4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554866,448,442 - 6,547,488 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554866,442,058 - 6,547,451 (+)NCBIChiLan1.0ChiLan1.0
NPHP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21222,234,457 - 222,370,369 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11220,876,170 - 221,012,339 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v014,620,593 - 4,756,363 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.115,878,739 - 6,012,869 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl15,878,739 - 6,012,864 (-)Ensemblpanpan1.1panPan2
NPHP4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1559,819,236 - 59,936,220 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl559,814,274 - 59,929,386 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha559,830,501 - 59,946,241 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0560,022,493 - 60,152,631 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl560,035,558 - 60,152,688 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1560,035,853 - 60,151,600 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0559,902,253 - 60,018,001 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0560,303,659 - 60,419,425 (-)NCBIUU_Cfam_GSD_1.0
Nphp4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505830,316,914 - 30,418,643 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936623802,152 - 904,198 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPHP4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120125,739,075 - 125,878,088 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20125,744,295 - 125,874,482 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605429,894,007 - 30,031,596 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nphp4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248185,327,038 - 5,432,901 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248185,325,946 - 5,432,290 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in NPHP4
2248 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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium
Low 3 3 3 4 1 21 2 3 1
Below cutoff 7 1 1 1 2 2

Sequence


RefSeq Acc Id: ENSSSCT00000022446   ⟹   ENSSSCP00000023406
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl666,815,281 - 66,928,146 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000070406   ⟹   ENSSSCP00000064629
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl666,815,282 - 66,920,591 (-)Ensembl
RefSeq Acc Id: XR_002344862
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1666,815,282 - 66,928,245 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002344863
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1666,815,282 - 66,927,802 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002344864
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1666,815,282 - 66,927,694 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002344865
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1666,815,282 - 66,928,245 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002344866
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1666,815,282 - 66,928,245 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002344867
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1666,815,282 - 66,928,245 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002344868
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1666,815,282 - 66,903,917 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002344869
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1666,815,282 - 66,903,021 (-)NCBI
Sequence:
Protein Sequences
Ensembl Protein ENSSSCP00000023406.3
RefSeq Acc Id: ENSSSCP00000064629   ⟸   ENSSSCT00000070406
RefSeq Acc Id: ENSSSCP00000023406   ⟸   ENSSSCT00000022446


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000029843 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000022446 ENTREZGENE
  ENSSSCT00000022446.3 UniProtKB/TrEMBL
InterPro NPHP4 UniProtKB/TrEMBL
NCBI Gene NPHP4 ENTREZGENE
PANTHER NEPHROCYSTIN-4 UniProtKB/TrEMBL
  PTHR31043 UniProtKB/TrEMBL
UniProt I3LH61_PIG UniProtKB/TrEMBL