Nicol1 (NELL2 interacting cell ontogeny regulator 1) - Rat Genome Database

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Gene: Nicol1 (NELL2 interacting cell ontogeny regulator 1) Rattus norvegicus
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Symbol: Nicol1
Name: NELL2 interacting cell ontogeny regulator 1
RGD ID: 1560394
Description: Predicted to enable mRNA 3'-UTR binding activity and transferrin receptor binding activity. Predicted to be involved in 3'-UTR-mediated mRNA stabilization and spermatogenesis. Predicted to be located in perinuclear region of cytoplasm. Predicted to be active in extracellular space. Orthologous to human NICOL1 (NELL2 interacting cell ontogeny regulator 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical LOC289728; hypothetical protein LOC289728; LOC289728; NELL2-interacting cell ontogeny regulator 1; neuropeptide-like protein C4orf48 homolog; RGD1560394; RGD1560394; uncharacterized protein LOC289728
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
GRCr81480,992,697 - 80,994,213 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1480,992,697 - 80,994,213 (-)EnsemblGRCr8
mRatBN7.21476,768,145 - 76,769,661 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1476,768,146 - 76,773,575 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1481,220,322 - 81,221,838 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01482,460,964 - 82,462,480 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01478,906,216 - 78,907,732 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01482,053,684 - 82,055,290 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1482,053,685 - 82,055,290 (-)Ensemblrn6Rnor6.0
Rnor_5.01482,737,924 - 82,739,530 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41482,462,073 - 82,463,678 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1475,691,720 - 75,693,325 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Nicol1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81480,992,697 - 80,994,213 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1480,992,697 - 80,994,213 (-)EnsemblGRCr8
mRatBN7.21476,768,145 - 76,769,661 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1476,768,146 - 76,773,575 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1481,220,322 - 81,221,838 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01482,460,964 - 82,462,480 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01478,906,216 - 78,907,732 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01482,053,684 - 82,055,290 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1482,053,685 - 82,055,290 (-)Ensemblrn6Rnor6.0
Rnor_5.01482,737,924 - 82,739,530 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41482,462,073 - 82,463,678 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1475,691,720 - 75,693,325 (-)NCBICelera
Cytogenetic Map14q21NCBI
NICOL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3842,036,554 - 2,043,964 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl42,040,628 - 2,043,964 (+)Ensemblhg38GRCh38
GRCh3742,043,722 - 2,045,691 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3642,013,487 - 2,015,495 (+)NCBIBuild 36Build 36hg18NCBI36
Celera41,955,927 - 1,957,904 (+)NCBICelera
Cytogenetic Map4p16.3NCBI
HuRef41,985,062 - 1,987,039 (+)NCBIHuRef
CHM1_142,042,359 - 2,044,336 (+)NCBICHM1_1
T2T-CHM13v2.042,034,123 - 2,042,451 (+)NCBIT2T-CHM13v2.0
Nicol1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39534,140,863 - 34,142,353 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl534,140,777 - 34,142,357 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38533,983,433 - 33,985,009 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl533,983,433 - 33,985,013 (+)Ensemblmm10GRCm38
MGSCv37534,326,123 - 34,327,655 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36534,300,331 - 34,301,865 (+)NCBIMGSCv36mm8
Celera531,453,190 - 31,454,732 (+)NCBICelera
Cytogenetic Map5B2NCBI
cM Map517.83NCBI
Nicol1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555141,200,721 - 1,213,789 (+)Ensembl
ChiLan1.0NW_0049555141,200,732 - 1,201,730 (+)NCBIChiLan1.0ChiLan1.0
NICOL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v232,374,830 - 2,376,832 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan142,311,264 - 2,313,277 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v042,184,128 - 2,186,148 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.142,092,442 - 2,094,564 (+)NCBIPanPan1.1PanPan1.1panPan2
NICOL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1362,119,568 - 62,121,981 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha364,637,548 - 64,639,826 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0362,595,193 - 62,597,474 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl362,595,199 - 62,597,448 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1362,087,758 - 62,090,033 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0362,291,418 - 62,293,695 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0362,651,433 - 62,653,711 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
NICOL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl81,054,236 - 1,058,200 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.181,055,115 - 1,058,203 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28641,957 - 645,882 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NICOL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12746,719,529 - 46,721,549 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660513,090,084 - 3,092,069 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nicol1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475525,477,323 - 25,478,735 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475525,477,354 - 25,478,742 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Nicol1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11170,884,469 - 70,886,079 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nicol1
10 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:138
Count of miRNA genes:105
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000058062
Prediction methods:Microtar, 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
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143802371083023710Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147764007196755654Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1459848686104848686Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1477914838104348525Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143900944484009444Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147297021087582095Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143067446985041098Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1474255551109089856Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147764007196755654Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143802371083023710Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1477640071100078267Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1460854936105854936Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1474255551109089856Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147764007196755654Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1459848686104848686Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147764007196755654Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144261625899224555Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143802371083023710Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)146592028399224555Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143941117087582095Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143802371083023710Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
9 6 44 137 55 54 24 25 24 6 178 92 2 121 49 83 30 15 15

Sequence


Ensembl Acc Id: ENSRNOT00000058062   ⟹   ENSRNOP00000054870
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1482,053,685 - 82,055,290 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100065   ⟹   ENSRNOP00000079921
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1476,768,146 - 76,773,575 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000146397   ⟹   ENSRNOP00000107084
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1480,992,697 - 80,994,213 (-)Ensembl
RefSeq Acc Id: NM_001401543   ⟹   NP_001388472
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81480,992,697 - 80,994,213 (-)NCBI
mRatBN7.21476,768,145 - 76,769,661 (-)NCBI
RefSeq Acc Id: NM_001401544   ⟹   NP_001388473
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81480,992,697 - 80,994,213 (-)NCBI
mRatBN7.21476,768,145 - 76,769,661 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001388472 (Get FASTA)   NCBI Sequence Viewer  
  NP_001388473 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM00109 (Get FASTA)   NCBI Sequence Viewer  
  EDM00110 (Get FASTA)   NCBI Sequence Viewer  
  EDM00111 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000107084
  ENSRNOP00000107084.1
Ensembl Acc Id: ENSRNOP00000054870   ⟸   ENSRNOT00000058062
Ensembl Acc Id: ENSRNOP00000079921   ⟸   ENSRNOT00000100065
RefSeq Acc Id: NP_001388472   ⟸   NM_001401543
- Peptide Label: precursor
- UniProtKB: A6IK47 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001388473   ⟸   NM_001401544
- Peptide Label: precursor
- UniProtKB: A6IK47 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000107084   ⟸   ENSRNOT00000146397

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZT05-F1-model_v2 AlphaFold D3ZT05 1-91 view protein structure

Transcriptome

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

Promoters
RGD ID:13699406
Promoter ID:EPDNEW_R9930
Type:single initiation site
Name:RGD1560394_1
Description:RGD1560394
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_6.01482,055,203 - 82,055,263EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560394 AgrOrtholog
BioCyc Gene G2FUF-15277 BioCyc
Ensembl Genes ENSRNOG00000038150 Ensembl
  ENSRNOG00000065022 Ensembl
  ENSRNOG00000074184 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000146397 ENTREZGENE
  ENSRNOT00000146397.1 UniProtKB/TrEMBL
InterPro Neuropep-like UniProtKB/TrEMBL
NCBI Gene 289728 ENTREZGENE
PANTHER NEUROPEPTIDE-LIKE PROTEIN C4ORF48 UniProtKB/TrEMBL
  PTHR35451 UniProtKB/TrEMBL
Pfam Neuropep_like UniProtKB/TrEMBL
PhenoGen Nicol1 PhenoGen
RatGTEx ENSRNOG00000038150 RatGTEx
  ENSRNOG00000065022 RatGTEx
  ENSRNOG00000074184 RatGTEx
UniProt A0ABK0L9J5_RAT UniProtKB/TrEMBL
  A6IK47 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-07-25 Nicol1  NELL2 interacting cell ontogeny regulator 1  RGD1560394  RGD1560394  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1560394  RGD1560394   RGD1560394_predicted  RGD1560394 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560394_predicted  RGD1560394 (predicted)  LOC289728  hypothetical LOC289728  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC289728  hypothetical LOC289728      Symbol and Name status set to provisional 70820 PROVISIONAL