Cryba4 (crystallin, beta A4) - Rat Genome Database

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Gene: Cryba4 (crystallin, beta A4) Rattus norvegicus
Analyze
Symbol: Cryba4
Name: crystallin, beta A4
RGD ID: 61962
Description: A structural constituent of eye lens. Predicted to be involved in lens development in camera-type eye and visual perception. Biomarker of cataract. Human ortholog(s) of this gene implicated in cataract 23. Orthologous to human CRYBA4 (crystallin beta A4); INTERACTS WITH acetamide; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: beta-A4 crystallin; beta-crystallin A4
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
GRCr81250,039,148 - 50,053,636 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1250,047,049 - 50,053,634 (+)EnsemblGRCr8
mRatBN7.21244,378,734 - 44,393,226 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1244,378,737 - 44,393,221 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1245,555,658 - 45,562,248 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01246,165,908 - 46,172,493 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01245,226,439 - 45,233,024 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01250,407,843 - 50,414,434 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1250,407,843 - 50,414,432 (+)Ensemblrn6Rnor6.0
Rnor_5.01252,158,613 - 52,170,763 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera1245,969,827 - 45,976,131 (+)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View
cataract  (IEP,ISO)
cataract 23  (ISO)
genetic disease  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Lens proteomics: analysis of rat crystallin sequences and two-dimensional electrophoresis map. Lampi KJ, etal., Invest Ophthalmol Vis Sci 2002 Jan;43(1):216-24.
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. Crystallin proteins in lenses of hereditary cataractous rat, ICR/f. Takeuchi N and Kamei A, Biol Pharm Bull. 2000 Mar;23(3):283-90.
11. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:8405363   PMID:16960806   PMID:31254514  


Genomics

Comparative Map Data
Cryba4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81250,039,148 - 50,053,636 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1250,047,049 - 50,053,634 (+)EnsemblGRCr8
mRatBN7.21244,378,734 - 44,393,226 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1244,378,737 - 44,393,221 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1245,555,658 - 45,562,248 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01246,165,908 - 46,172,493 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01245,226,439 - 45,233,024 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01250,407,843 - 50,414,434 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1250,407,843 - 50,414,432 (+)Ensemblrn6Rnor6.0
Rnor_5.01252,158,613 - 52,170,763 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera1245,969,827 - 45,976,131 (+)NCBICelera
Cytogenetic Map12q16NCBI
CRYBA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382226,590,220 - 26,630,669 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2226,621,963 - 26,630,669 (+)Ensemblhg38GRCh38
GRCh372227,017,927 - 27,026,633 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362225,347,928 - 25,356,636 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342225,342,481 - 25,351,186NCBI
Celera2210,821,730 - 10,830,436 (+)NCBICelera
Cytogenetic Map22q12.1ENTREZGENE
HuRef229,965,449 - 9,974,165 (+)NCBIHuRef
CHM1_12226,977,460 - 26,986,228 (+)NCBICHM1_1
T2T-CHM13v2.02227,070,652 - 27,093,286 (+)NCBIT2T-CHM13v2.0
Cryba4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395112,394,358 - 112,411,411 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5112,394,359 - 112,400,384 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm385112,246,492 - 112,263,625 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5112,246,493 - 112,252,518 (-)Ensemblmm10GRCm38
MGSCv375112,675,553 - 112,681,522 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv365112,486,836 - 112,492,805 (-)NCBIMGSCv36mm8
MGSCv361379,940,098 - 79,946,067 (+)NCBIMGSCv36mm8
Celera5109,366,099 - 109,372,068 (-)NCBICelera
Cytogenetic Map5FNCBI
cM Map554.62NCBI
Cryba4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554551,176,668 - 1,187,731 (+)Ensembl
ChiLan1.0NW_0049554551,176,668 - 1,187,731 (+)NCBIChiLan1.0ChiLan1.0
CRYBA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22336,627,106 - 36,639,664 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12239,326,228 - 39,338,114 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0227,683,356 - 7,692,532 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12225,405,980 - 25,414,643 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2225,405,980 - 25,414,643 (+)EnsemblpanPan2panpan1.1
CRYBA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12620,272,962 - 20,280,368 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2620,273,739 - 20,280,367 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2620,137,450 - 20,144,081 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02620,615,647 - 20,643,528 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2620,606,735 - 20,643,527 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12620,358,447 - 20,365,059 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02620,609,294 - 20,615,918 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02620,679,442 - 20,686,080 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cryba4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118114,650,331 - 114,657,220 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366571,213,333 - 1,221,392 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366571,213,487 - 1,220,376 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CRYBA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1444,194,592 - 44,219,163 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11444,212,690 - 44,219,163 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21447,091,993 - 47,099,095 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CRYBA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1199,491,105 - 9,528,986 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666045116,573,468 - 116,582,107 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cryba4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247473,142,982 - 3,147,900 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247473,142,982 - 3,147,900 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Cryba4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11641,717,887 - 41,730,347 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:60
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000073763
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
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121613502952308831Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122480502252308831Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121120049452308831Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121618743851213550Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
1331763Wbc2White blood cell count QTL 23.162leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)121120049452308831Rat
8693635Alc28Alcohol consumption QTL 282.70.439drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122871771850386405Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)61120049452308831Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122598935552308831Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121847304152308831Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123776414551558799Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049752308831Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121526424852308831Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121847304152308831Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)121174352852308831Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12563330650633306Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121613502952308831Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)123370043251558799Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121618743852308831Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)124413955852308831Rat

Markers in Region
RH138337  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21244,391,482 - 44,393,065 (+)MAPPERmRatBN7.2
Rnor_6.01250,412,691 - 50,414,273NCBIRnor6.0
Rnor_5.01252,169,020 - 52,170,602UniSTSRnor5.0
Celera1245,974,390 - 45,975,972UniSTS
RH 3.4 Map12776.22UniSTS


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 2 66 113 54 54 23 87 23 6 277 178 10 91 59 88 31 4 4

Sequence


Ensembl Acc Id: ENSRNOT00000073763   ⟹   ENSRNOP00000066572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1250,047,049 - 50,053,634 (+)Ensembl
mRatBN7.2 Ensembl1244,378,737 - 44,393,221 (+)Ensembl
Rnor_6.0 Ensembl1250,407,843 - 50,414,432 (+)Ensembl
RefSeq Acc Id: NM_031689   ⟹   NP_113877
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81250,047,049 - 50,053,634 (+)NCBI
mRatBN7.21244,386,637 - 44,393,224 (+)NCBI
Rnor_6.01250,407,843 - 50,414,432 (+)NCBI
Rnor_5.01252,158,613 - 52,170,763 (+)NCBI
Celera1245,969,827 - 45,976,131 (+)RGD
Sequence:
RefSeq Acc Id: XM_017598447   ⟹   XP_017453936
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81250,047,815 - 50,053,636 (+)NCBI
mRatBN7.21244,387,405 - 44,393,226 (+)NCBI
Rnor_6.01250,407,915 - 50,414,434 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039089722   ⟹   XP_038945650
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81250,039,148 - 50,053,636 (+)NCBI
mRatBN7.21244,378,734 - 44,393,226 (+)NCBI
RefSeq Acc Id: XM_039089723   ⟹   XP_038945651
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81250,047,806 - 50,053,636 (+)NCBI
mRatBN7.21244,387,396 - 44,393,226 (+)NCBI
RefSeq Acc Id: NP_113877   ⟸   NM_031689
- UniProtKB: P56374 (UniProtKB/Swiss-Prot),   A6J267 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453936   ⟸   XM_017598447
- Peptide Label: isoform X1
- UniProtKB: P56374 (UniProtKB/Swiss-Prot),   A6J267 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000066572   ⟸   ENSRNOT00000073763
RefSeq Acc Id: XP_038945650   ⟸   XM_039089722
- Peptide Label: isoform X1
- UniProtKB: P56374 (UniProtKB/Swiss-Prot),   A6J267 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038945651   ⟸   XM_039089723
- Peptide Label: isoform X2
Protein Domains
Beta/gamma crystallin 'Greek key'

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P56374-F1-model_v2 AlphaFold P56374 1-196 view protein structure

Transcriptome

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

Promoters
RGD ID:13698730
Promoter ID:EPDNEW_R9255
Type:single initiation site
Name:Cryba4_1
Description:crystallin, beta A4
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_6.01250,407,842 - 50,407,902EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61962 AgrOrtholog
BioCyc Gene G2FUF-18863 BioCyc
Ensembl Genes ENSRNOG00000049770 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000073763 ENTREZGENE
  ENSRNOT00000073763.2 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:64348 UniProtKB/Swiss-Prot
NCBI Gene 64348 ENTREZGENE
PANTHER BETA/GAMMA CRYSTALLIN UniProtKB/Swiss-Prot
  PTHR11818:SF19 UniProtKB/Swiss-Prot
Pfam Crystall UniProtKB/Swiss-Prot
PhenoGen Cryba4 PhenoGen
PRINTS BGCRYSTALLIN UniProtKB/Swiss-Prot
PROSITE CRYSTALLIN_BETA_GAMMA UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000049770 RatGTEx
SMART XTALbg UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49695 UniProtKB/Swiss-Prot
TIGR TC217020
UniProt A6J267 ENTREZGENE, UniProtKB/TrEMBL
  CRBA4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Cryba4  crystallin, beta A4      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference