Nyx (nyctalopin) - Rat Genome Database

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Gene: Nyx (nyctalopin) Rattus norvegicus
Analyze
Symbol: Nyx
Name: nyctalopin
RGD ID: 1561300
Description: Predicted to act upstream of or within visual perception. Predicted to be active in extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in congenital stationary night blindness 1A and night blindness. Orthologous to human NYX (nyctalopin); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC302516; RGD1561300; similar to Nyctalopin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X11,953,680 - 11,974,716 (-)NCBIGRCr8
mRatBN7.2X9,280,864 - 9,301,900 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX9,280,864 - 9,301,900 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX9,464,782 - 9,485,829 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X12,961,944 - 12,982,989 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X9,233,454 - 9,254,432 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X10,197,547 - 10,218,583 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX10,197,547 - 10,218,583 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X10,996,027 - 11,017,063 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X21,293,033 - 21,314,069 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX9,819,177 - 9,840,154 (-)NCBICelera
Cytogenetic MapXq12NCBI
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

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Mutations in NYX, encoding the leucine-rich proteoglycan nyctalopin, cause X-linked complete congenital stationary night blindness. Bech-Hansen NT, etal., Nat Genet. 2000 Nov;26(3):319-23.
2. 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.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12506099   PMID:15359216   PMID:18246026  


Genomics

Comparative Map Data
Nyx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X11,953,680 - 11,974,716 (-)NCBIGRCr8
mRatBN7.2X9,280,864 - 9,301,900 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX9,280,864 - 9,301,900 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX9,464,782 - 9,485,829 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X12,961,944 - 12,982,989 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X9,233,454 - 9,254,432 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X10,197,547 - 10,218,583 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX10,197,547 - 10,218,583 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X10,996,027 - 11,017,063 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X21,293,033 - 21,314,069 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX9,819,177 - 9,840,154 (-)NCBICelera
Cytogenetic MapXq12NCBI
NYX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X41,447,343 - 41,475,652 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX41,447,343 - 41,475,710 (+)EnsemblGRCh38hg38GRCh38
GRCh37X41,306,596 - 41,334,905 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X41,191,631 - 41,219,907 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X41,062,940 - 41,091,217NCBI
CeleraX45,447,487 - 45,475,680 (+)NCBICelera
Cytogenetic MapXp11.4NCBI
HuRefX39,038,027 - 39,066,404 (+)NCBIHuRef
CHM1_1X41,339,448 - 41,367,628 (+)NCBICHM1_1
T2T-CHM13v2.0X40,851,430 - 40,879,740 (+)NCBIT2T-CHM13v2.0
Nyx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X13,327,097 - 13,359,059 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX13,332,349 - 13,355,552 (+)EnsemblGRCm39 Ensembl
GRCm38X13,461,090 - 13,492,820 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX13,466,110 - 13,489,313 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X13,044,798 - 13,066,439 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X12,623,066 - 12,646,271 (+)NCBIMGSCv36mm8
CeleraX11,137,534 - 11,158,769 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX8.37NCBI
Nyx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555651,258,724 - 1,262,283 (-)NCBIChiLan1.0ChiLan1.0
NYX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X43,097,839 - 43,127,194 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X43,101,212 - 43,130,567 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X33,899,010 - 33,928,363 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X41,617,437 - 41,619,042 (+)NCBIpanpan1.1PanPan1.1panPan2
NYX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X35,849,190 - 35,868,048 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX23,197,511 - 23,216,363 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X35,900,163 - 35,921,854 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X35,977,493 - 35,996,375 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X35,949,667 - 35,968,502 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X35,992,826 - 36,011,691 (+)NCBIUU_Cfam_GSD_1.0
Nyx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X28,049,848 - 28,070,063 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365027,890,535 - 7,910,986 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365027,890,582 - 7,909,157 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NYX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX37,080,278 - 37,105,510 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X37,080,197 - 37,105,513 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X41,299,214 - 41,325,323 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NYX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X38,642,393 - 38,665,534 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660763,821,357 - 3,846,087 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nyx
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476214,157,116 - 14,183,611 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476214,154,655 - 14,183,822 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nyx
56 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:174
Count of miRNA genes:141
Interacting mature miRNAs:153
Transcripts:ENSRNOT00000013382
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
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
70166Bp65Blood pressure QTL 655.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144797211374346Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat

Markers in Region
BE097638  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,280,546 - 9,280,740 (+)MAPPERmRatBN7.2
Rnor_6.0X10,197,230 - 10,197,423NCBIRnor6.0
Rnor_5.0X10,995,710 - 10,995,903UniSTSRnor5.0
RGSC_v3.4X21,292,716 - 21,292,909UniSTSRGSC3.4
CeleraX9,818,860 - 9,819,053UniSTS
RH 3.4 MapX0.0UniSTS
Cytogenetic MapXq12UniSTS


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 6
Low 5 26 19 2
Below cutoff 1 36 8 2 8 2 7 7 40 22 20 9 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013382   ⟹   ENSRNOP00000013382
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX9,280,864 - 9,301,900 (-)Ensembl
Rnor_6.0 EnsemblX10,197,547 - 10,218,583 (-)Ensembl
RefSeq Acc Id: NM_001100967   ⟹   NP_001094437
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X11,953,680 - 11,974,716 (-)NCBI
mRatBN7.2X9,280,864 - 9,301,900 (-)NCBI
Rnor_6.0X10,197,547 - 10,218,583 (-)NCBI
Rnor_5.0X10,996,027 - 11,017,063 (-)NCBI
RGSC_v3.4X21,293,033 - 21,314,069 (-)RGD
CeleraX9,819,177 - 9,840,154 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001094437 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ABD52240 (Get FASTA)   NCBI Sequence Viewer  
  EDL97655 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000013382
  ENSRNOP00000013382.5
Reference Protein Sequences
RefSeq Acc Id: NP_001094437   ⟸   NM_001100967
- Peptide Label: precursor
- UniProtKB: A1XIQ3 (UniProtKB/TrEMBL),   A6JZY0 (UniProtKB/TrEMBL),   F7EKE5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013382   ⟸   ENSRNOT00000013382
Protein Domains
LRRCT   LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A1XIQ3-F1-model_v2 AlphaFold A1XIQ3 1-476 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:1561300 AgrOrtholog
BioCyc Gene G2FUF-3089 BioCyc
Ensembl Genes ENSRNOG00000009646 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013382 ENTREZGENE
  ENSRNOT00000013382.6 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro Cys-rich_flank_reg_C UniProtKB/TrEMBL
  L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR-contain_N UniProtKB/TrEMBL
KEGG Report rno:302516 UniProtKB/TrEMBL
NCBI Gene 302516 ENTREZGENE
PANTHER NYCTALOPIN UniProtKB/TrEMBL
  SLIT RELATED LEUCINE-RICH REPEAT NEURONAL PROTEIN UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
PhenoGen Nyx PhenoGen
RatGTEx ENSRNOG00000009646 RatGTEx
SMART LRR_TYP UniProtKB/TrEMBL
  LRRCT UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A1XIQ3 ENTREZGENE
  A6JZY0 ENTREZGENE, UniProtKB/TrEMBL
  F7EKE5 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A1XIQ3 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Nyx  nyctalopin   Nyx_predicted  nyctalopin (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Nyx_predicted  nyctalopin (predicted)  RGD1561300_predicted  similar to Nyctalopin (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1561300_predicted  similar to Nyctalopin (predicted)  LOC302516  similar to Nyctalopin  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302516  similar to Nyctalopin      Symbol and Name status set to provisional 70820 PROVISIONAL