Nrl (neural retina leucine zipper) - Rat Genome Database

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Gene: Nrl (neural retina leucine zipper) Rattus norvegicus
Analyze
Symbol: Nrl
Name: neural retina leucine zipper
RGD ID: 1305197
Description: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; leucine zipper domain binding activity; and promoter-specific chromatin binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II and retinal rod cell development. Predicted to act upstream of or within positive regulation of gene expression and positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in retinitis pigmentosa and retinitis pigmentosa 27. Orthologous to human NRL (neural retina leucine zipper); INTERACTS WITH 6-propyl-2-thiouracil; all-trans-retinoic acid; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC290221; neural retina leucine zipper gene; neural retina-specific leucine zipper protein
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
GRCr81532,977,023 - 32,981,442 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1532,977,035 - 32,981,442 (-)EnsemblGRCr8
mRatBN7.21529,007,059 - 29,011,480 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,008,104 - 29,009,832 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1530,853,805 - 30,855,533 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,001,015 - 32,002,743 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,243,363 - 30,245,091 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,197,115 - 34,201,408 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,197,193 - 34,198,921 (-)Ensemblrn6Rnor6.0
Rnor_5.01538,087,364 - 38,108,942 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41533,649,927 - 33,656,045 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1528,584,069 - 28,585,797 (-)NCBICelera
RGSC_v3.11533,667,545 - 33,669,274 (-)NCBI
Cytogenetic Map15p13NCBI
JBrowse:




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

Cellular Component
cytoplasm  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Novel mutations in the NRL gene and associated clinical findings in patients with dominant retinitis pigmentosa. DeAngelis MM, etal., Arch Ophthalmol. 2002 Mar;120(3):369-75.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8552602   PMID:10887186   PMID:11477108   PMID:11694879   PMID:15163632   PMID:15689355   PMID:16854989   PMID:17335001   PMID:21981118  


Genomics

Comparative Map Data
Nrl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81532,977,023 - 32,981,442 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1532,977,035 - 32,981,442 (-)EnsemblGRCr8
mRatBN7.21529,007,059 - 29,011,480 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,008,104 - 29,009,832 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1530,853,805 - 30,855,533 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,001,015 - 32,002,743 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,243,363 - 30,245,091 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,197,115 - 34,201,408 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,197,193 - 34,198,921 (-)Ensemblrn6Rnor6.0
Rnor_5.01538,087,364 - 38,108,942 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41533,649,927 - 33,656,045 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1528,584,069 - 28,585,797 (-)NCBICelera
RGSC_v3.11533,667,545 - 33,669,274 (-)NCBI
Cytogenetic Map15p13NCBI
NRL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381424,078,662 - 24,114,949 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1424,078,662 - 24,115,010 (-)Ensemblhg38GRCh38
GRCh371424,547,871 - 24,584,158 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361423,619,156 - 23,623,672 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341423,619,215 - 23,654,063NCBI
Celera144,413,793 - 4,418,309 (-)NCBICelera
Cytogenetic Map14q11.2-q12NCBI
HuRef144,664,249 - 4,668,765 (-)NCBIHuRef
CHM1_11424,547,991 - 24,552,507 (-)NCBICHM1_1
T2T-CHM13v2.01418,276,978 - 18,313,262 (-)NCBIT2T-CHM13v2.0
Nrl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391455,756,973 - 55,762,438 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1455,756,435 - 55,762,438 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381455,518,978 - 55,524,981 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1455,518,978 - 55,524,981 (-)Ensemblmm10GRCm38
MGSCv371456,137,815 - 56,143,802 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361454,473,049 - 54,478,262 (-)NCBIMGSCv36mm8
Celera1453,323,817 - 53,329,813 (-)NCBICelera
Cytogenetic Map14C3NCBI
cM Map1428.19NCBI
Nrl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540936,310,932 - 36,313,893 (+)Ensembl
ChiLan1.0NW_00495540936,279,996 - 36,313,824 (+)NCBIChiLan1.0ChiLan1.0
NRL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21525,436,209 - 25,469,236 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11424,652,701 - 24,685,728 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0144,858,105 - 4,891,207 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11422,982,367 - 23,015,912 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1422,982,367 - 22,998,187 (-)EnsemblpanPan2panpan1.1
NRL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.184,086,487 - 4,090,373 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl84,086,508 - 4,089,216 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha84,009,349 - 4,011,899 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.084,198,235 - 4,200,786 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl84,197,290 - 4,199,944 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.183,888,893 - 3,891,443 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.083,950,633 - 3,953,183 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.084,212,744 - 4,215,293 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nrl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864035,934,928 - 35,966,368 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936722447,967 - 454,553 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936722448,006 - 454,064 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NRL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl775,206,719 - 75,210,529 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1775,199,048 - 75,211,655 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2780,470,343 - 80,482,968 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NRL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1241,064,266 - 1,100,995 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl241,064,664 - 1,066,278 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603612,744,482 - 12,758,698 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nrl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248208,444,687 - 8,449,354 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248208,436,469 - 8,449,354 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Nrl
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11269,486,146 - 69,488,147 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nrl
54 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:12
Count of miRNA genes:12
Interacting mature miRNAs:12
Transcripts:ENSRNOT00000024991
Prediction methods:Miranda, Rnahybrid
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
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15231575947315759Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15139411584Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15144836456Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152272835342072050Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat

Markers in Region
RH139326  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21529,006,582 - 29,006,823 (+)MAPPERmRatBN7.2
Rnor_6.01534,195,648 - 34,195,888NCBIRnor6.0
Rnor_5.01538,086,259 - 38,086,499UniSTSRnor5.0
RGSC_v3.41533,649,978 - 33,650,218UniSTSRGSC3.4
Celera1528,582,616 - 28,582,856UniSTS
RH 3.4 Map21537.1UniSTS
Cytogenetic Map15p13UniSTS
RH139409  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21529,007,108 - 29,007,239 (+)MAPPERmRatBN7.2
Rnor_6.01534,196,174 - 34,196,304NCBIRnor6.0
Rnor_5.01538,086,785 - 38,086,915UniSTSRnor5.0
RGSC_v3.41533,650,504 - 33,650,634UniSTSRGSC3.4
Celera1528,583,142 - 28,583,272UniSTS
Cytogenetic Map15p13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
2 9 80 35 31 24 8 24 3 48 21 74 1 17 7 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000024991   ⟹   ENSRNOP00000024991
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1532,977,035 - 32,981,442 (-)Ensembl
mRatBN7.2 Ensembl1529,008,104 - 29,009,832 (-)Ensembl
Rnor_6.0 Ensembl1534,197,193 - 34,198,921 (-)Ensembl
RefSeq Acc Id: NM_001106036   ⟹   NP_001099506
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81532,977,023 - 32,981,442 (-)NCBI
mRatBN7.21529,007,059 - 29,011,480 (-)NCBI
Rnor_6.01534,197,193 - 34,198,921 (-)NCBI
Rnor_5.01538,087,364 - 38,108,942 (-)NCBI
RGSC_v3.41533,649,927 - 33,656,045 (-)RGD
Celera1528,584,069 - 28,585,797 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063274123   ⟹   XP_063130193
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81532,977,023 - 32,980,128 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099506 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130193 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM14235 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000024991
  ENSRNOP00000024991.2
RefSeq Acc Id: NP_001099506   ⟸   NM_001106036
- UniProtKB: D4ACF4 (UniProtKB/TrEMBL),   A6KH06 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000024991   ⟸   ENSRNOT00000024991
RefSeq Acc Id: XP_063130193   ⟸   XM_063274123
- Peptide Label: isoform X1
- UniProtKB: A6KH06 (UniProtKB/TrEMBL),   D4ACF4 (UniProtKB/TrEMBL)
Protein Domains
bZIP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACF4-F1-model_v2 AlphaFold D4ACF4 1-238 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:1305197 AgrOrtholog
BioCyc Gene G2FUF-13720 BioCyc
Ensembl Genes ENSRNOG00000018528 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024991 ENTREZGENE
  ENSRNOT00000024991.6 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.170 UniProtKB/TrEMBL
InterPro bZIP_sf UniProtKB/TrEMBL
  Euk_TF_DNA-bd UniProtKB/TrEMBL
  Maf_TF_N UniProtKB/TrEMBL
  TF_bZIP UniProtKB/TrEMBL
  TF_Maf UniProtKB/TrEMBL
  Transciption_factor_Maf UniProtKB/TrEMBL
KEGG Report rno:290221 UniProtKB/TrEMBL
NCBI Gene 290221 ENTREZGENE
PANTHER PTHR10129 UniProtKB/TrEMBL
  PTHR10129:SF24 UniProtKB/TrEMBL
Pfam bZIP_Maf UniProtKB/TrEMBL
  Maf_N UniProtKB/TrEMBL
PhenoGen Nrl PhenoGen
PROSITE BZIP UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018528 RatGTEx
SMART BRLZ UniProtKB/TrEMBL
Superfamily-SCOP Euk_transcr_DNA UniProtKB/TrEMBL
  SSF57959 UniProtKB/TrEMBL
UniProt A6KH06 ENTREZGENE, UniProtKB/TrEMBL
  D4ACF4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-10 Nrl  neural retina leucine zipper  Nrl  neural retina leucine zipper gene   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Nrl  neural retina leucine zipper gene   Nrl_predicted  neural retina leucine zipper gene (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Nrl_predicted  neural retina leucine zipper gene (predicted)      Symbol and Name status set to approved 70820 APPROVED