Chic2 (cysteine-rich hydrophobic domain 2) - Rat Genome Database

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Gene: Chic2 (cysteine-rich hydrophobic domain 2) Rattus norvegicus
Analyze
Symbol: Chic2
Name: cysteine-rich hydrophobic domain 2
RGD ID: 1309278
Description: Predicted to be located in Golgi apparatus. Predicted to be active in Golgi-associated vesicle and plasma membrane. Human ortholog(s) of this gene implicated in acute myeloid leukemia. Orthologous to human CHIC2 (cysteine rich hydrophobic domain 2); INTERACTS WITH 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cysteine-rich hydrophobic domain 2 protein; cysteine-rich hydrophobic domain-containing protein 2
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
GRCr81433,511,839 - 33,546,181 (+)NCBIGRCr8
mRatBN7.21433,157,669 - 33,192,015 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1433,157,537 - 33,191,895 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1433,507,861 - 33,542,251 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01434,815,670 - 34,849,824 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01433,300,926 - 33,335,318 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01435,683,657 - 35,718,005 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1435,683,442 - 35,717,922 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01435,512,033 - 35,546,381 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41435,522,470 - 35,558,067 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11435,499,310 - 35,557,069 (+)NCBI
Celera1432,427,860 - 32,462,239 (+)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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. 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.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8889548   PMID:11257495   PMID:22871113  


Genomics

Comparative Map Data
Chic2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81433,511,839 - 33,546,181 (+)NCBIGRCr8
mRatBN7.21433,157,669 - 33,192,015 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1433,157,537 - 33,191,895 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1433,507,861 - 33,542,251 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01434,815,670 - 34,849,824 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01433,300,926 - 33,335,318 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01435,683,657 - 35,718,005 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1435,683,442 - 35,717,922 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01435,512,033 - 35,546,381 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41435,522,470 - 35,558,067 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11435,499,310 - 35,557,069 (+)NCBI
Celera1432,427,860 - 32,462,239 (+)NCBICelera
Cytogenetic Map14p11NCBI
CHIC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38454,009,789 - 54,091,879 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl454,009,789 - 54,064,605 (-)EnsemblGRCh38hg38GRCh38
GRCh37454,875,956 - 54,930,772 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36454,570,713 - 54,625,545 (-)NCBINCBI36Build 36hg18NCBI36
Build 34454,716,885 - 54,771,716NCBI
Celera452,375,088 - 52,430,482 (-)NCBICelera
Cytogenetic Map4q12NCBI
HuRef450,822,904 - 50,877,817 (-)NCBIHuRef
CHM1_1454,911,655 - 54,966,517 (-)NCBICHM1_1
T2T-CHM13v2.0457,497,038 - 57,579,148 (-)NCBIT2T-CHM13v2.0
Chic2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39575,165,665 - 75,205,302 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl575,158,649 - 75,205,435 (-)EnsemblGRCm39 Ensembl
GRCm38575,005,004 - 75,044,641 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl574,997,988 - 75,044,774 (-)EnsemblGRCm38mm10GRCm38
MGSCv37575,402,449 - 75,440,651 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36575,288,121 - 75,326,323 (-)NCBIMGSCv36mm8
Celera572,289,910 - 72,328,910 (-)NCBICelera
Cytogenetic Map5C3.3NCBI
cM Map539.54NCBI
Chic2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544716,786,136 - 16,804,361 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544716,723,598 - 16,805,878 (+)NCBIChiLan1.0ChiLan1.0
CHIC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2375,725,640 - 75,785,464 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1475,934,039 - 76,019,672 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0469,875,762 - 69,933,360 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1476,435,107 - 76,490,712 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl476,435,107 - 76,490,371 (+)Ensemblpanpan1.1panPan2
CHIC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11346,558,657 - 46,606,226 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1346,560,009 - 46,607,959 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1346,512,630 - 46,564,868 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01347,165,483 - 47,217,744 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1347,169,583 - 47,217,685 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11346,838,016 - 46,890,246 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01346,370,185 - 46,422,417 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01347,243,242 - 47,295,476 (-)NCBIUU_Cfam_GSD_1.0
Chic2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528529,630,105 - 29,669,530 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648216,629,317 - 16,667,950 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648216,628,705 - 16,668,132 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHIC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl840,780,889 - 40,846,577 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1840,781,365 - 40,846,715 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2842,834,328 - 42,889,022 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHIC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1714,479,200 - 14,533,848 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606615,317,890 - 15,373,397 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chic2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476115,427,923 - 15,465,447 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476115,427,835 - 15,482,244 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chic2
188 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:425
Count of miRNA genes:238
Interacting mature miRNAs:267
Transcripts:ENSRNOT00000003085
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
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat


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 3 30 43 28 19 28 1 1 68 27 41 11 1
Low 13 14 13 13 7 10 6 8 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003085   ⟹   ENSRNOP00000003085
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1433,157,537 - 33,191,895 (+)Ensembl
Rnor_6.0 Ensembl1435,683,442 - 35,717,922 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100515   ⟹   ENSRNOP00000085584
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1433,157,537 - 33,190,923 (+)Ensembl
RefSeq Acc Id: NM_001105736   ⟹   NP_001099206
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81433,511,839 - 33,546,181 (+)NCBI
mRatBN7.21433,157,669 - 33,192,015 (+)NCBI
Rnor_6.01435,683,657 - 35,718,005 (+)NCBI
Rnor_5.01435,512,033 - 35,546,381 (+)NCBI
RGSC_v3.41435,522,470 - 35,558,067 (+)RGD
Celera1432,427,860 - 32,462,239 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001099206   ⟸   NM_001105736
- UniProtKB: G3V6A1 (UniProtKB/TrEMBL),   A6JD10 (UniProtKB/TrEMBL),   B6RGM6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003085   ⟸   ENSRNOT00000003085
RefSeq Acc Id: ENSRNOP00000085584   ⟸   ENSRNOT00000100515
Protein Domains
Golgin subfamily A member 7/ERF4

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6A1-F1-model_v2 AlphaFold G3V6A1 1-165 view protein structure

Transcriptome

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

Promoters
RGD ID:13699282
Promoter ID:EPDNEW_R9807
Type:initiation region
Name:Chic2_1
Description:cysteine-rich hydrophobic domain 2
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_6.01435,683,447 - 35,683,507EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309278 AgrOrtholog
BioCyc Gene G2FUF-15920 BioCyc
Ensembl Genes ENSRNOG00000002267 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003085 ENTREZGENE
  ENSRNOT00000003085.8 UniProtKB/TrEMBL
  ENSRNOT00000100515.1 UniProtKB/TrEMBL
InterPro CHIC1/2 UniProtKB/TrEMBL
  Golgin_A_7/ERF4 UniProtKB/TrEMBL
KEGG Report rno:83835 UniProtKB/TrEMBL
NCBI Gene 83835 ENTREZGENE
PANTHER CYSTEINE-RICH HYDROPHOBIC DOMAIN-CONTAINING PROTEIN 2 UniProtKB/TrEMBL
  PTHR13005 UniProtKB/TrEMBL
Pfam Erf4 UniProtKB/TrEMBL
PhenoGen Chic2 PhenoGen
RatGTEx ENSRNOG00000002267 RatGTEx
UniProt A0A8I6A1Z0_RAT UniProtKB/TrEMBL
  A6JD10 ENTREZGENE, UniProtKB/TrEMBL
  B6RGM6 ENTREZGENE, UniProtKB/TrEMBL
  B6RGM8_RAT UniProtKB/TrEMBL
  G3V6A1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Chic2  cysteine-rich hydrophobic domain 2   Chic2_predicted  cysteine-rich hydrophobic domain 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Chic2_predicted  cysteine-rich hydrophobic domain 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED