Chic1 (cysteine-rich hydrophobic domain 1) - Rat Genome Database

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Gene: Chic1 (cysteine-rich hydrophobic domain 1) Rattus norvegicus
Analyze
Symbol: Chic1
Name: cysteine-rich hydrophobic domain 1
RGD ID: 1589722
Description: Orthologous to human CHIC1 (cysteine rich hydrophobic domain 1); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cysteine-rich hydrophobic domain 1 protein; cysteine-rich hydrophobic domain-containing protein 1; LOC363484; similar to cysteine-rich hydrophobic domain 1
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
GRCr8X72,427,851 - 72,471,924 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX72,427,851 - 72,471,924 (+)EnsemblGRCr8
mRatBN7.2X68,362,014 - 68,406,155 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX68,361,969 - 68,437,887 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX69,871,276 - 69,915,347 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X73,371,522 - 73,415,588 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X70,932,706 - 70,976,774 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X74,205,649 - 74,250,613 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX74,200,972 - 74,244,846 (+)Ensemblrn6Rnor6.0
Rnor_5.0X75,012,806 - 75,056,683 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X91,321,388 - 91,359,707 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX69,729,260 - 69,773,943 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Chic1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X72,427,851 - 72,471,924 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX72,427,851 - 72,471,924 (+)EnsemblGRCr8
mRatBN7.2X68,362,014 - 68,406,155 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX68,361,969 - 68,437,887 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX69,871,276 - 69,915,347 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X73,371,522 - 73,415,588 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X70,932,706 - 70,976,774 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X74,205,649 - 74,250,613 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX74,200,972 - 74,244,846 (+)Ensemblrn6Rnor6.0
Rnor_5.0X75,012,806 - 75,056,683 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X91,321,388 - 91,359,707 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX69,729,260 - 69,773,943 (+)NCBICelera
Cytogenetic MapXq22NCBI
CHIC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X73,563,148 - 73,687,111 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX73,563,197 - 73,687,111 (+)Ensemblhg38GRCh38
GRCh37X72,782,984 - 72,906,946 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X72,699,709 - 72,823,662 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34X72,683,810 - 72,684,147NCBI
CeleraX73,066,460 - 73,190,414 (+)NCBICelera
Cytogenetic MapXq13.2NCBI
HuRefX66,415,920 - 66,540,598 (+)NCBIHuRef
CHM1_1X72,675,825 - 72,799,741 (+)NCBICHM1_1
T2T-CHM13v2.0X71,996,510 - 72,120,438 (+)NCBIT2T-CHM13v2.0
Chic1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X102,400,009 - 102,452,698 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX102,400,082 - 102,439,698 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X103,356,403 - 103,409,092 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX103,356,476 - 103,396,092 (+)Ensemblmm10GRCm38
MGSCv37X100,551,815 - 100,591,457 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X99,559,275 - 99,592,761 (+)NCBIMGSCv36mm8
CeleraX90,259,397 - 90,298,960 (+)NCBICelera
Cytogenetic MapXDNCBI
cM MapX46.08NCBI
Chic1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955591580,764 - 653,469 (+)Ensembl
ChiLan1.0NW_004955591581,415 - 659,840 (+)NCBIChiLan1.0ChiLan1.0
CHIC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X73,237,784 - 73,353,774 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X73,244,031 - 73,357,382 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X62,809,942 - 62,923,345 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X72,932,415 - 73,047,011 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX72,932,415 - 73,040,911 (+)EnsemblpanPan2panpan1.1
CHIC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X57,198,789 - 57,274,007 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX57,198,944 - 57,254,522 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX48,375,504 - 48,450,432 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X58,408,824 - 58,483,808 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX58,408,972 - 58,483,911 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X56,155,622 - 56,230,554 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X57,733,664 - 57,808,690 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X57,340,553 - 57,415,496 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Chic1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X44,440,494 - 44,550,163 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936683397,568 - 463,398 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936683397,609 - 491,491 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHIC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX59,176,604 - 59,230,783 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X59,176,650 - 59,230,332 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X67,050,837 - 67,104,842 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHIC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X63,124,857 - 63,244,752 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX63,124,918 - 63,241,072 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660655,070,964 - 5,213,179 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chic1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248367,868,057 - 7,961,990 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248367,868,157 - 8,012,983 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Chic1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X68,413,100 - 68,455,348 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Chic1
69 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:21
Count of miRNA genes:20
Interacting mature miRNAs:21
Transcripts:ENSRNOT00000015693
Prediction methods:Miranda, Pita, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X4493088389930883Rat


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
16 10 66 164 91 90 59 89 59 6 350 186 11 143 81 91 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000003922   ⟹   ENSRNOP00000003922
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,423,719 - 68,437,887 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076490
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX74,201,157 - 74,211,588 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076956   ⟹   ENSRNOP00000068153
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,362,027 - 68,437,704 (+)Ensembl
Rnor_6.0 EnsemblX74,200,972 - 74,244,846 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000077003   ⟹   ENSRNOP00000067927
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,361,969 - 68,437,887 (+)Ensembl
Rnor_6.0 EnsemblX74,205,842 - 74,244,376 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000098584   ⟹   ENSRNOP00000093183
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,427,451 - 68,435,419 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101872   ⟹   ENSRNOP00000078564
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,361,969 - 68,402,819 (+)Ensembl
RefSeq Acc Id: NM_001401184   ⟹   NP_001388113
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X72,427,851 - 72,471,924 (+)NCBI
mRatBN7.2X68,362,079 - 68,406,155 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001388113 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07191 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000078564
  ENSRNOP00000078564.1
Ensembl Acc Id: ENSRNOP00000067927   ⟸   ENSRNOT00000077003
Ensembl Acc Id: ENSRNOP00000068153   ⟸   ENSRNOT00000076956
Ensembl Acc Id: ENSRNOP00000003922   ⟸   ENSRNOT00000003922
Ensembl Acc Id: ENSRNOP00000078564   ⟸   ENSRNOT00000101872
Ensembl Acc Id: ENSRNOP00000093183   ⟸   ENSRNOT00000098584
RefSeq Acc Id: NP_001388113   ⟸   NM_001401184
- UniProtKB: A0A8I5ZL82 (UniProtKB/TrEMBL),   A6IUY9 (UniProtKB/TrEMBL)
Protein Domains
Golgin subfamily A member 7/ERF4

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A096MJJ5-F1-model_v2 AlphaFold A0A096MJJ5 1-226 view protein structure

Transcriptome

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

Promoters
RGD ID:13701892
Promoter ID:EPDNEW_R12413
Type:single initiation site
Name:Chic1_1
Description:cysteine-rich hydrophobic domain 1
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_6.0X74,205,842 - 74,205,902EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589722 AgrOrtholog
BioCyc Gene G2FUF-2029 BioCyc
Ensembl Genes ENSRNOG00000037919 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000101872 ENTREZGENE
  ENSRNOT00000101872.2 UniProtKB/TrEMBL
InterPro CHIC1/2 UniProtKB/TrEMBL
  Golgin_A_7/ERF4 UniProtKB/TrEMBL
NCBI Gene 363484 ENTREZGENE
PANTHER CYSTEINE-RICH HYDROPHOBIC DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  PTHR13005 UniProtKB/TrEMBL
Pfam Erf4 UniProtKB/TrEMBL
PhenoGen Chic1 PhenoGen
RatGTEx ENSRNOG00000037919 RatGTEx
UniProt A0A8I5ZL82 ENTREZGENE, UniProtKB/TrEMBL
  A6IUY9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Chic1  cysteine-rich hydrophobic domain 1  LOC363484  similar to cysteine-rich hydrophobic domain 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC363484  similar to cysteine-rich hydrophobic domain 1      Symbol and Name status set to provisional 70820 PROVISIONAL