Cryaa (crystallin, alpha A) - Rat Genome Database

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Gene: Cryaa (crystallin, alpha A) Rattus norvegicus
Symbol: Cryaa
Name: crystallin, alpha A
RGD ID: 2413
Description: Enables identical protein binding activity. Involved in several processes, including multicellular organism aging; response to hydrogen peroxide; and response to lead ion. Located in cytoplasm. Used to study cataract. Biomarker of cataract; galactosemia; and ocular hypertension. Human ortholog(s) of this gene implicated in cataract 9 multiple types. Orthologous to human CRYAA (crystallin alpha A); PARTICIPATES IN Endoplasmic Reticulum-associated degradation pathway; INTERACTS WITH (R)-lipoic acid; (R,R,R)-alpha-tocopherol; 5-azacytidine.
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: VALIDATED
Previously known as: Acry-1; alpha-crystallin A chain; Crya1; Crystallin alpha polypeptide A; Crystallin, alpha polypeptide A
RGD Orthologs
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.2209,783,605 - 9,787,351 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl209,783,605 - 9,787,349 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2010,485,297 - 10,489,042 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0209,846,484 - 9,850,229 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02010,315,168 - 10,318,913 (+)NCBIRnor_WKY
Rnor_6.02010,438,444 - 10,442,189 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2010,438,444 - 10,442,187 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02012,621,549 - 12,625,628 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2011,297,259 - 11,301,004 (+)NCBICelera
RH 3.4 Map20134.02RGD
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View

References - curated
# Reference Title Reference Citation
1. Selective association of crystallins with lens 'native' membrane during dynamic cataractogenesis. Cenedella RJ and Fleschner CR, Curr Eye Res. 1992 Aug;11(8):801-15.
2. Comparison of post-translational modifications of alpha A-crystallin from normal and hereditary cataract rats. Fujii N, etal., Amino Acids. 2004 Mar;26(2):147-52. Epub 2003 Dec 18.
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. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
6. Cell death triggered by a novel mutation in the alphaA-crystallin gene underlies autosomal dominant cataract linked to chromosome 21q. Mackay DS, etal., Eur J Hum Genet 2003 Oct;11(10):784-93.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Cataract-linked gammaD-crystallin mutants have weak affinity to lens chaperones alpha-crystallins. Mishra S, etal., FEBS Lett. 2012 Feb 17;586(4):330-6. doi: 10.1016/j.febslet.2012.01.019. Epub 2012 Jan 28.
9. Proteomic analysis of rat retina in a steroid-induced ocular hypertension model: potential vulnerability to oxidative stress. Miyara N, etal., Jpn J Ophthalmol. 2008 Mar-Apr;52(2):84-90. Epub 2008 Apr 30.
10. An unusually long non-coding region in rat lens alpha-crystallin messenger RNA. Moormann RJ, etal., Nucleic Acids Res 1981 Oct 10;9(19):4813-22.
11. Mouse Genome Database (MGD) Mouse Genome Database (MGD)
12. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Pb2+ exposure alters the lens alpha A-crystallin protein profile in vivo and induces cataract formation in lens organ culture. Neal R, etal., Toxicology. 2005 Aug 15;212(1):1-9.
14. Ontogeny of alpha-crystallin subunits in the lens of human and rat embryos. Oguni M, etal., Cell Tissue Res. 1994 Apr;276(1):151-4.
15. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
16. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
17. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. Changes in physicochemical parameters and alpha-crystallin expression in the lens during cataract development in OXYS rats. 5. Rumyantseva YV, etal., Biochemistry (Mosc). 2008 Nov;73(11):1176-82.
20. Phe71 is essential for chaperone-like function in alpha A-crystallin. Santhoshkumar P and Sharma KK, J Biol Chem. 2001 Dec 14;276(50):47094-9. Epub 2001 Oct 11.
21. alpha A-crystallin is expressed in non-ocular tissues. Srinivasan AN, etal., J Biol Chem 1992 Nov 15;267(32):23337-41.
22. Influence of the C-terminal residues on oligomerization of alpha A-crystallin. Thampi P and Abraham EC, Biochemistry. 2003 Oct 14;42(40):11857-63.
23. Translocation of small heat shock proteins to the actin cytoskeleton upon proteasomal inhibition. Verschuure P, etal., J Mol Cell Cardiol. 2002 Feb;34(2):117-28.
24. Phosphorylation of alpha-crystallin in rat lenses is stimulated by H2O2 but phosphorylation has no effect on chaperone activity. Wang K, etal., Exp Eye Res. 1995 Jul;61(1):115-24.
25. Crystallin mRNA concentrations and distribution in lens of normal and galactosemic rats. Implications in development of sugar cataracts. Wen Y, etal., Invest Ophthalmol Vis Sci. 1991 Apr;32(5):1638-47.
Additional References at PubMed
PMID:699911   PMID:2294971   PMID:8812430   PMID:8875649   PMID:8943244   PMID:9023351   PMID:9467006   PMID:9813033   PMID:11687536   PMID:12235146   PMID:12477932   PMID:12546709  
PMID:12584250   PMID:12601044   PMID:14690441   PMID:14752512   PMID:16303126   PMID:16309625   PMID:16439475   PMID:16675842   PMID:16799046   PMID:17176090   PMID:17438522   PMID:17893660  
PMID:18056999   PMID:18158587   PMID:18191123   PMID:18407550   PMID:18551258   PMID:18587492   PMID:19464326   PMID:19558454   PMID:19651604   PMID:20682783   PMID:21311744   PMID:21677790  
PMID:22085609   PMID:23071119   PMID:23142719   PMID:23376485   PMID:23508955   PMID:25416956   PMID:26378715  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.2209,783,605 - 9,787,351 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl209,783,605 - 9,787,349 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2010,485,297 - 10,489,042 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0209,846,484 - 9,850,229 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02010,315,168 - 10,318,913 (+)NCBIRnor_WKY
Rnor_6.02010,438,444 - 10,442,189 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2010,438,444 - 10,442,187 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02012,621,549 - 12,625,628 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2011,297,259 - 11,301,004 (+)NCBICelera
RH 3.4 Map20134.02RGD
Cytogenetic Map20p12NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh382143,169,008 - 43,172,810 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2143,169,008 - 43,172,805 (+)EnsemblGRCh38hg38GRCh38
GRCh372144,589,118 - 44,592,920 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362143,462,210 - 43,465,982 (+)NCBINCBI36Build 36hg18NCBI36
Build 342143,462,209 - 43,465,982NCBI
Celera2129,741,819 - 29,745,592 (+)NCBICelera
Cytogenetic Map21q22.3NCBI
HuRef2130,007,222 - 30,011,008 (+)NCBIHuRef
CHM1_12144,149,981 - 44,153,753 (+)NCBICHM1_1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391731,896,905 - 31,900,704 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1731,896,781 - 31,900,707 (+)EnsemblGRCm39 Ensembl
GRCm381731,677,931 - 31,681,730 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1731,677,807 - 31,681,733 (+)EnsemblGRCm38mm10GRCm38
MGSCv371731,814,890 - 31,818,669 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361731,406,661 - 31,410,057 (+)NCBIMGSCv36mm8
Celera1732,595,462 - 32,599,241 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.09NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_00495540738,880,086 - 38,925,642 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540738,880,088 - 38,892,946 (-)NCBIChiLan1.0ChiLan1.0
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.13137,307,070 - 37,310,262 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3137,307,093 - 37,310,247 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3136,462,427 - 36,465,619 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03136,850,477 - 36,853,680 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3136,850,500 - 36,853,665 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13136,719,304 - 36,722,496 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03136,704,182 - 36,707,379 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03137,196,540 - 37,199,740 (+)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_02440497136,532,632 - 36,536,019 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936500931,754 - 935,296 (-)EnsemblSpeTri2.0
SpeTri2.0NW_004936500931,804 - 935,185 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl13206,293,849 - 206,297,015 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113206,293,877 - 206,297,050 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_00462474527,637,267 - 27,639,371 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474527,636,932 - 27,639,814 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Cryaa
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:130
Count of miRNA genes:59
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000071248, ENSRNOT00000075545
Prediction methods: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 (
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
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2209,787,194 - 9,787,291 (+)MAPPERmRatBN7.2
Rnor_6.02010,442,033 - 10,442,129NCBIRnor6.0
Rnor_5.02012,625,472 - 12,625,568UniSTSRnor5.0
Celera2011,300,848 - 11,300,944UniSTS
RH 3.4 Map20134.02UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02010,438,587 - 10,440,172NCBIRnor6.0
Rnor_5.02012,622,026 - 12,623,611UniSTSRnor5.0
Celera2011,297,402 - 11,298,987UniSTS


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 endocrine system exocrine system hemolymphoid system hepatobiliary system musculoskeletal system nervous system renal system reproductive system respiratory system
Medium 6
Low 2 7 12 7 5
Below cutoff 12 4 1 4 1 31 19 14 6


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071248   ⟹   ENSRNOP00000067332
RefSeq Status:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl209,783,605 - 9,787,349 (+)Ensembl
Rnor_6.0 Ensembl2010,438,444 - 10,442,187 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075545   ⟹   ENSRNOP00000065714
RefSeq Status:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2010,438,489 - 10,442,181 (+)Ensembl
RefSeq Acc Id: NM_001289737   ⟹   NP_001276666
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
mRatBN7.2209,783,652 - 9,787,343 (+)NCBI
Rnor_6.02010,438,489 - 10,442,181 (+)NCBI
Celera2011,297,304 - 11,300,996 (+)NCBI
RefSeq Acc Id: NM_012534   ⟹   NP_036666
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
mRatBN7.2209,783,605 - 9,787,351 (+)NCBI
Rnor_6.02010,438,444 - 10,442,189 (+)NCBI
Rnor_5.02012,621,549 - 12,625,628 (+)NCBI
Celera2011,297,259 - 11,301,004 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036666   ⟸   NM_012534
- Peptide Label: isoform 1
- UniProtKB: P24623 (UniProtKB/Swiss-Prot),   A0JN13 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001276666   ⟸   NM_001289737
- Peptide Label: isoform 2
- UniProtKB: P24623 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065714   ⟸   ENSRNOT00000075545
RefSeq Acc Id: ENSRNOP00000067332   ⟸   ENSRNOT00000071248
Protein Domains

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P24623-F1-model_v2 AlphaFold P24623 1-196 view protein structure


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

RGD ID:13701480
Promoter ID:EPDNEW_R12003
Type:single initiation site
Description:crystallin, alpha A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Experiment Methods:Single-end sequencing.
Rat AssemblyChrPosition (strand)Source
Rnor_6.02010,438,435 - 10,438,495EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2413 AgrOrtholog
BioCyc Gene G2FUF-4304 BioCyc
Ensembl Genes ENSRNOG00000047175 Ensembl
Gene3D-CATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro A-crystallin/Hsp20_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Alpha-crystallin/HSP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Alpha-crystallin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HSP20-like_chaperone UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24273 UniProtKB/Swiss-Prot
PANTHER PTHR45640 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR45640:SF14 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Crystallin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HSP20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cryaa PhenoGen
Superfamily-SCOP SSF49764 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt Secondary P02490 UniProtKB/Swiss-Prot
  P02496 UniProtKB/Swiss-Prot
  P82532 UniProtKB/Swiss-Prot
  Q61444 UniProtKB/Swiss-Prot

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

RGD Curation Notes
Note Type Note Reference
gene_disease mutation of the human homolog is associated with an autosomal dominant form of nuclear cataract 727765
gene_expression expressed in brain, liver, lung, spleen, skin, and small intestine 727765
gene_product may be a member of the small-heat-shock protein (sHSP) family of molecular chaperones 728218