Crygd (crystallin, gamma D) - Rat Genome Database

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Gene: Crygd (crystallin, gamma D) Rattus norvegicus
Analyze
Symbol: Crygd
Name: crystallin, gamma D
RGD ID: 2422
Description: A structural constituent of eye lens. Involved in lens fiber cell differentiation and response to peptide hormone. Predicted to be located in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in cataract 4 multiple types and cataract 7. Orthologous to human CRYGD (crystallin gamma D); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Cryg4; Crystallin gamma polypeptide 4; Crystallin, gamma polypeptide 4; gamma-crystallin 2-2; gamma-crystallin D; gamma-D-crystallin; Len
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8973,935,798 - 73,937,409 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl973,935,795 - 73,937,808 (-)EnsemblGRCr8
mRatBN7.2966,442,057 - 66,443,668 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl966,442,054 - 66,444,067 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx974,955,290 - 74,956,901 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0980,090,585 - 80,092,196 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0978,499,024 - 78,500,635 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0971,776,568 - 71,778,323 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl971,764,318 - 71,778,323 (-)Ensemblrn6Rnor6.0
Rnor_5.0970,790,042 - 70,803,964 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4963,711,051 - 63,712,662 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera963,837,702 - 63,839,313 (-)NCBICelera
RGSC_v3.1963,858,032 - 63,859,644 (-)NCBI
Cytogenetic Map9q32NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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

Biological Process

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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Nucleotide sequence of the rat gamma-crystallin gene region and comparison with an orthologous human region. den Dunnen JT, etal., Gene 1989 May 30;78(2):201-13.
2. The sequence of regulatory events controlling the expression of the gamma D-crystallin gene during fibroblast growth factor-mediated rat lens fiber cell differentiation. Dirks RP, etal., Dev Biol. 1996 Jan 10;173(1):14-25.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Gamma-D crystallin gene (CRYGD) mutation causes autosomal dominant congenital cerulean cataracts. Nandrot E, etal., J Med Genet. 2003 Apr;40(4):262-7.
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. High level expression of rat gamma-D-crystallin in Escherichia coli. Ooki K, etal., Biochimie 1994;76(5):398-403.
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Comprehensive gene review and curation RGD comprehensive gene curation
14. Differential synthesis of crystallins in the developing rat eye lens. Voorter CE, etal., Exp Eye Res. 1990 Apr;50(4):429-37.
Additional References at PubMed
PMID:3783678   PMID:8943244   PMID:9927684   PMID:10704279   PMID:12011157   PMID:15037589   PMID:17652744   PMID:23404175  


Genomics

Comparative Map Data
Crygd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8973,935,798 - 73,937,409 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl973,935,795 - 73,937,808 (-)EnsemblGRCr8
mRatBN7.2966,442,057 - 66,443,668 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl966,442,054 - 66,444,067 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx974,955,290 - 74,956,901 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0980,090,585 - 80,092,196 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0978,499,024 - 78,500,635 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0971,776,568 - 71,778,323 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl971,764,318 - 71,778,323 (-)Ensemblrn6Rnor6.0
Rnor_5.0970,790,042 - 70,803,964 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4963,711,051 - 63,712,662 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera963,837,702 - 63,839,313 (-)NCBICelera
RGSC_v3.1963,858,032 - 63,859,644 (-)NCBI
Cytogenetic Map9q32NCBI
CRYGD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382208,121,607 - 208,124,524 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2208,121,607 - 208,124,524 (-)Ensemblhg38GRCh38
GRCh372208,986,331 - 208,989,248 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362208,694,577 - 208,697,458 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342208,811,837 - 208,814,719NCBI
Celera2202,754,599 - 202,757,581 (-)NCBICelera
Cytogenetic Map2q33.3NCBI
HuRef2200,834,785 - 200,837,767 (-)NCBIHuRef
CHM1_12208,992,125 - 208,995,102 (-)NCBICHM1_1
T2T-CHM13v2.02208,601,624 - 208,604,541 (-)NCBIT2T-CHM13v2.0
Crygd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39165,101,001 - 65,102,598 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl165,101,031 - 65,102,611 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38165,061,838 - 65,063,440 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl165,061,872 - 65,063,452 (-)Ensemblmm10GRCm38
MGSCv37165,108,412 - 65,110,014 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36164,996,119 - 64,997,685 (-)NCBIMGSCv36mm8
Celera165,554,907 - 65,556,511 (-)NCBICelera
Cytogenetic Map1C2NCBI
cM Map132.8NCBI
LOC100978046
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213110,727,056 - 110,730,505 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B110,742,032 - 110,745,236 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B95,352,149 - 95,356,237 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B213,476,336 - 213,479,279 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B213,476,336 - 213,479,279 (-)EnsemblpanPan2panpan1.1
CRYGD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13716,424,884 - 16,433,479 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3717,307,807 - 17,316,401 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03716,360,607 - 16,369,192 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3716,360,585 - 16,362,369 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13716,305,289 - 16,313,857 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03716,278,488 - 16,287,054 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03716,287,674 - 16,296,225 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC100519628
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15111,242,765 - 111,244,775 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.115111,242,765 - 111,244,738 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LOC103217728
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11093,903,173 - 93,908,652 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040105,459,291 - 105,463,860 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Crygd
17 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:76
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000050886, ENSRNOT00000064562
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
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)94002992585029925Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)92956766474567664Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)94445825685262605Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92956766483835942Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)94172029586720295Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1581517Bp284Blood pressure QTL 284arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)93922018684220186Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)94002992585029925Rat
1598849Memor17Memory QTL 172.2exploratory 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)95746049778547958Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93496059079960590Rat

Markers in Region
D9Wox8  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8973,969,072 - 73,969,193 (+)Marker Load Pipeline
mRatBN7.2966,475,328 - 66,475,449 (+)MAPPERmRatBN7.2
Rnor_6.0971,821,468 - 71,821,588NCBIRnor6.0
Rnor_5.0970,749,367 - 70,749,487UniSTSRnor5.0
Celera963,870,765 - 63,870,885UniSTS
RH 3.4 Map9566.7RGD
RH 3.4 Map9566.7UniSTS
RH 2.0 Map9621.6RGD
D9Mit2  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8973,930,789 - 73,930,979 (+)Marker Load Pipeline
mRatBN7.2966,437,052 - 66,437,242 (+)MAPPERmRatBN7.2
Rnor_6.0971,771,288 - 71,771,476NCBIRnor6.0
Rnor_5.0970,797,216 - 70,797,404UniSTSRnor5.0
RGSC_v3.4963,705,762 - 63,705,951UniSTSRGSC3.4
RGSC_v3.4963,705,761 - 63,705,951RGDRGSC3.4
Celera963,832,694 - 63,832,883UniSTS
RGSC_v3.1963,852,743 - 63,852,933RGD
RH 3.4 Map9588.2UniSTS
RH 3.4 Map9588.2RGD
RH 2.0 Map9632.5RGD
SHRSP x BN Map945.5498RGD
FHH x ACI Map942.29RGD
Cytogenetic Map9 RGD


Expression

RNA-SEQ Expression

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
11 61 90 27 34 18 20 18 4 132 94 4 84 12 33 16 10 10

Sequence


Ensembl Acc Id: ENSRNOT00000050886   ⟹   ENSRNOP00000051301
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl973,935,798 - 73,937,409 (-)Ensembl
mRatBN7.2 Ensembl966,442,057 - 66,443,668 (-)Ensembl
Rnor_6.0 Ensembl971,776,568 - 71,778,323 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000064562   ⟹   ENSRNOP00000060248
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl971,764,318 - 71,778,188 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000107623   ⟹   ENSRNOP00000082230
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl973,935,795 - 73,937,808 (-)Ensembl
mRatBN7.2 Ensembl966,442,054 - 66,444,067 (-)Ensembl
RefSeq Acc Id: NM_033095   ⟹   NP_149086
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8973,935,798 - 73,937,409 (-)NCBI
mRatBN7.2966,442,057 - 66,443,668 (-)NCBI
Rnor_6.0971,776,568 - 71,778,323 (-)NCBI
Rnor_5.0970,790,042 - 70,803,964 (+)NCBI
RGSC_v3.4963,711,051 - 63,712,662 (-)RGD
Celera963,837,702 - 63,839,313 (-)RGD
Sequence:
RefSeq Acc Id: XM_063266627   ⟹   XP_063122697
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8973,935,798 - 73,937,389 (-)NCBI
Protein Sequences
Protein RefSeqs NP_149086 (Get FASTA)   NCBI Sequence Viewer  
  XP_063122697 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40984 (Get FASTA)   NCBI Sequence Viewer  
  CAA40458 (Get FASTA)   NCBI Sequence Viewer  
  EDL98869 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000051301
  ENSRNOP00000051301.3
GenBank Protein P10067 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_149086   ⟸   NM_033095
- UniProtKB: P10067 (UniProtKB/Swiss-Prot),   A6IPJ1 (UniProtKB/TrEMBL),   A0A8I5ZXH9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000051301   ⟸   ENSRNOT00000050886
Ensembl Acc Id: ENSRNOP00000060248   ⟸   ENSRNOT00000064562
Ensembl Acc Id: ENSRNOP00000082230   ⟸   ENSRNOT00000107623
RefSeq Acc Id: XP_063122697   ⟸   XM_063266627
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZXH9 (UniProtKB/TrEMBL)
Protein Domains
Beta/gamma crystallin 'Greek key'

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P10067-F1-model_v2 AlphaFold P10067 1-174 view protein structure

Transcriptome

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

Promoters
RGD ID:13696718
Promoter ID:EPDNEW_R7242
Type:single initiation site
Name:Crygd_1
Description:crystallin, gamma D
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_6.0971,778,323 - 71,778,383EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2422 AgrOrtholog
BioCyc Gene G2FUF-27305 BioCyc
Ensembl Genes ENSRNOG00000032219 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000050886 ENTREZGENE
  ENSRNOT00000050886.3 UniProtKB/Swiss-Prot
Gene3D-CATH Crystallins UniProtKB/Swiss-Prot
InterPro Beta/Gamma-Crystallin UniProtKB/Swiss-Prot
  Beta/gamma_crystallin UniProtKB/Swiss-Prot
  G_crystallin-like UniProtKB/Swiss-Prot
KEGG Report rno:24278 UniProtKB/Swiss-Prot
NCBI Gene 24278 ENTREZGENE
PANTHER BETA/GAMMA CRYSTALLIN UniProtKB/Swiss-Prot
  GAMMA-CRYSTALLIN D UniProtKB/Swiss-Prot
Pfam Crystall UniProtKB/Swiss-Prot
PhenoGen Crygd PhenoGen
PRINTS BGCRYSTALLIN UniProtKB/Swiss-Prot
PROSITE CRYSTALLIN_BETA_GAMMA UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000032219 RatGTEx
SMART XTALbg UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49695 UniProtKB/Swiss-Prot
UniProt A0A8I5ZXH9 ENTREZGENE, UniProtKB/TrEMBL
  A6IPJ1 ENTREZGENE, UniProtKB/TrEMBL
  CRGD_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-11-06 Crygd  crystallin, gamma D    Crystallin, gamma polypeptide 4  Name updated 625702 APPROVED
2002-06-10 Crygd  Crystallin, gamma polypeptide 4      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease may be involved in cataract formation 1298817
gene_expression expressed in lens of eye 1298817