YBX3 (Y-box binding protein 3) - Rat Genome Database

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Gene: YBX3 (Y-box binding protein 3) Homo sapiens
Analyze
Symbol: YBX3
Name: Y-box binding protein 3
RGD ID: 733766
HGNC Page HGNC
Description: Enables RNA binding activity. Involved in cellular hyperosmotic response; cellular response to tumor necrosis factor; and negative regulation of programmed cell death. Located in cytosol; INTERACTS WITH 17beta-estradiol; 2-hydroxypropanoic acid; 3-isobutyl-1-methyl-7H-xanthine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cold shock domain protein A; cold shock domain-containing protein A; cold-shock domain containing A1; cold-shock domain protein A; CSDA; CSDA1; DBPA; DNA-binding protein A; single-strand DNA-binding protein NF-GMB; Y box binding protein 3; Y-box-binding protein 3; ZO-1-associated nucleic acid-binding protein; ZONAB
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Related Pseudogenes: YBX3P1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1210,699,089 - 10,723,323 (-)EnsemblGRCh38hg38GRCh38
GRCh381210,699,084 - 10,723,442 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371210,851,688 - 10,875,922 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361210,742,955 - 10,767,171 (-)NCBINCBI36hg18NCBI36
Build 341210,742,955 - 10,767,171NCBI
Celera1216,000,000 - 16,024,276 (-)NCBI
Cytogenetic Map12p13.2NCBI
HuRef1210,580,443 - 10,604,713 (-)NCBIHuRef
CHM1_11210,821,053 - 10,845,329 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (ISO)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
3H-1,2-dithiole-3-thione  (ISO)
4,4'-sulfonyldiphenol  (EXP)
4-hydroxynon-2-enal  (EXP)
6-propyl-2-thiouracil  (ISO)
acrolein  (EXP)
acrylamide  (ISO)
aflatoxin B1  (EXP,ISO)
alpha-pinene  (EXP)
ammonium chloride  (ISO)
arsenite(3-)  (EXP)
atrazine  (ISO)
beauvericin  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (ISO)
cadmium dichloride  (EXP)
candesartan  (ISO)
carbon nanotube  (ISO)
chloropicrin  (EXP)
cisplatin  (EXP)
cobalt dichloride  (EXP)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (EXP)
Cuprizon  (ISO)
cyclosporin A  (EXP,ISO)
dexamethasone  (EXP)
dibutyl phthalate  (ISO)
dicrotophos  (EXP)
dorsomorphin  (EXP)
doxorubicin  (ISO)
elemental selenium  (EXP)
endosulfan  (ISO)
flutamide  (ISO)
fructose  (ISO)
griseofulvin  (ISO)
indometacin  (EXP)
ivermectin  (EXP)
ketamine  (ISO)
methotrexate  (ISO)
methylmercury chloride  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (ISO)
ozone  (EXP)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (ISO)
phenobarbital  (ISO)
phenol red  (EXP)
phenylmercury acetate  (EXP)
pirinixic acid  (ISO)
piroxicam  (EXP)
propiconazole  (ISO)
rac-lactic acid  (EXP)
raloxifene  (ISO)
resveratrol  (ISO)
SB 431542  (EXP)
selenium atom  (EXP)
sodium arsenite  (EXP)
sodium fluoride  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (EXP)
tetrachloromethane  (ISO)
trimellitic anhydride  (ISO)
urethane  (EXP)
vinclozolin  (ISO)
vitamin E  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:2977358   PMID:7628487   PMID:8710501   PMID:8871564   PMID:9442396   PMID:10100871   PMID:10343102   PMID:11799066   PMID:12239625   PMID:12477932   PMID:14728692   PMID:15302935  
PMID:15313206   PMID:15489334   PMID:15592429   PMID:16094384   PMID:16159877   PMID:16198352   PMID:16344560   PMID:16508013   PMID:17081983   PMID:17158914   PMID:17620599   PMID:17643375  
PMID:18029348   PMID:19240061   PMID:19274049   PMID:19322201   PMID:19328795   PMID:19369198   PMID:19710015   PMID:19749785   PMID:19805454   PMID:20020773   PMID:20133480   PMID:20431927  
PMID:21081503   PMID:21145461   PMID:21182205   PMID:21282530   PMID:21473684   PMID:21642987   PMID:21873635   PMID:22159460   PMID:22658674   PMID:22681889   PMID:22711822   PMID:22863883  
PMID:22939629   PMID:22990118   PMID:23084401   PMID:23151878   PMID:23398456   PMID:23443559   PMID:23463506   PMID:23602568   PMID:23752268   PMID:24244333   PMID:24457600   PMID:24817634  
PMID:24885929   PMID:25315684   PMID:25324306   PMID:25437307   PMID:25593058   PMID:25681748   PMID:25798074   PMID:25852190   PMID:26167880   PMID:26170170   PMID:26209609   PMID:26344197  
PMID:26381412   PMID:26496610   PMID:26527279   PMID:26549023   PMID:26627737   PMID:26725010   PMID:26777405   PMID:26816005   PMID:26949251   PMID:27025967   PMID:27430286   PMID:27569444  
PMID:27591049   PMID:27609421   PMID:28027390   PMID:28225217   PMID:28302793   PMID:28431233   PMID:28514442   PMID:28515276   PMID:28561026   PMID:28581483   PMID:28712289   PMID:28902428  
PMID:29053956   PMID:29117863   PMID:29227750   PMID:29229926   PMID:29298432   PMID:29331416   PMID:29395067   PMID:29467282   PMID:29507755   PMID:29509190   PMID:29669786   PMID:29777862  
PMID:29802200   PMID:29845934   PMID:29884807   PMID:30209976   PMID:30320910   PMID:30425250   PMID:30442762   PMID:30462309   PMID:30773093   PMID:30784285   PMID:30833792   PMID:30890647  
PMID:30940648   PMID:30948266   PMID:30997501   PMID:31048545   PMID:31091453   PMID:31152661   PMID:31189097   PMID:31239290   PMID:31253590   PMID:31586073   PMID:31640799   PMID:31665637  
PMID:31944153   PMID:31980649   PMID:32129710   PMID:32241891   PMID:32553055   PMID:32572027   PMID:32652867   PMID:32780723   PMID:32788342   PMID:32807901   PMID:32877691   PMID:32939012  
PMID:32994395   PMID:33060197   PMID:33277362   PMID:34079125  


Genomics

Comparative Map Data
YBX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1210,699,089 - 10,723,323 (-)EnsemblGRCh38hg38GRCh38
GRCh381210,699,084 - 10,723,442 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371210,851,688 - 10,875,922 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361210,742,955 - 10,767,171 (-)NCBINCBI36hg18NCBI36
Build 341210,742,955 - 10,767,171NCBI
Celera1216,000,000 - 16,024,276 (-)NCBI
Cytogenetic Map12p13.2NCBI
HuRef1210,580,443 - 10,604,713 (-)NCBIHuRef
CHM1_11210,821,053 - 10,845,329 (-)NCBICHM1_1
Ybx3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396131,341,821 - 131,365,413 (-)NCBIGRCm39mm39
GRCm39 Ensembl6131,341,818 - 131,365,439 (-)Ensembl
GRCm386131,364,858 - 131,388,450 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6131,364,855 - 131,388,476 (-)EnsemblGRCm38mm10GRCm38
MGSCv376131,314,876 - 131,338,468 (-)NCBIGRCm37mm9NCBIm37
MGSCv366131,330,551 - 131,354,143 (-)NCBImm8
Celera6136,414,596 - 136,438,226 (-)NCBICelera
Cytogenetic Map6F3NCBI
Ybx3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24165,129,747 - 165,153,101 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4165,129,758 - 165,153,161 (-)Ensembl
Rnor_6.04165,606,819 - 165,630,041 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4165,606,819 - 165,630,118 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04228,170,272 - 228,193,525 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44169,076,517 - 169,099,849 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14169,321,476 - 169,344,762 (-)NCBI
Celera4153,733,515 - 153,756,519 (-)NCBICelera
Cytogenetic Map4q42NCBI
Ybx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554137,089,719 - 7,108,473 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554137,090,085 - 7,111,542 (+)NCBIChiLan1.0ChiLan1.0
YBX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11210,994,177 - 11,018,504 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1210,996,380 - 11,018,172 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01210,728,049 - 10,752,267 (-)NCBIMhudiblu_PPA_v0panPan3
YBX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12735,043,756 - 35,066,230 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2735,043,699 - 35,066,227 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2711,465,924 - 11,493,283 (-)NCBI
ROS_Cfam_1.02735,383,798 - 35,411,218 (+)NCBI
UMICH_Zoey_3.12735,266,703 - 35,294,044 (+)NCBI
UNSW_CanFamBas_1.02735,211,037 - 35,238,385 (+)NCBI
UU_Cfam_GSD_1.02711,081,610 - 11,108,979 (-)NCBI
YBX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl561,337,863 - 61,361,280 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1561,337,868 - 61,361,269 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2564,060,833 - 64,084,239 (+)NCBISscrofa10.2Sscrofa10.2susScr3
YBX3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11110,498,162 - 10,522,432 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1110,500,361 - 10,522,226 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660892,576,328 - 2,600,838 (-)NCBIVero_WHO_p1.0

Position Markers
RH92531  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371210,877,662 - 10,877,794UniSTSGRCh37
Build 361210,768,929 - 10,769,061RGDNCBI36
Celera1216,025,985 - 16,026,117RGD
Cytogenetic Map12p13.1UniSTS
HuRef1210,606,423 - 10,606,555UniSTS
GeneMap99-GB4 RH Map1262.08UniSTS
RH69102  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371631,579,552 - 31,579,708UniSTSGRCh37
Build 361631,487,053 - 31,487,209RGDNCBI36
Cytogenetic Map16p11.2UniSTS
Cytogenetic Map12p13.1UniSTS
HuRef1629,139,932 - 29,140,088UniSTS
G61989  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371631,579,426 - 31,579,605UniSTSGRCh37
GRCh371210,852,009 - 10,852,188UniSTSGRCh37
Build 361210,743,276 - 10,743,455RGDNCBI36
Celera1216,000,333 - 16,000,512RGD
Cytogenetic Map16p11.2UniSTS
Cytogenetic Map12p13.1UniSTS
HuRef1629,139,806 - 29,139,985UniSTS
HuRef1210,580,776 - 10,580,955UniSTS
G62320  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371210,858,049 - 10,858,239UniSTSGRCh37
Build 361210,749,316 - 10,749,506RGDNCBI36
Celera1216,006,373 - 16,006,563RGD
Cytogenetic Map12p13.1UniSTS
HuRef1210,586,811 - 10,587,001UniSTS
D16S2544E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371631,579,890 - 31,579,977UniSTSGRCh37
Build 361631,487,391 - 31,487,478RGDNCBI36
Cytogenetic Map16p11.2UniSTS
Cytogenetic Map12p13.1UniSTS
HuRef1629,140,270 - 29,140,357UniSTS
IB391  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371631,580,362 - 31,580,534UniSTSGRCh37
Build 361631,487,863 - 31,488,035RGDNCBI36
Cytogenetic Map16p11.2UniSTS
Cytogenetic Map12p13.1UniSTS
HuRef1629,140,742 - 29,140,914UniSTS
TNG Radiation Hybrid Map1617633.0UniSTS
Stanford-G3 RH Map161660.0UniSTS
GeneMap99-G3 RH Map161620.0UniSTS
G07129  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371631,579,620 - 31,579,722UniSTSGRCh37
Build 361631,487,121 - 31,487,223RGDNCBI36
Cytogenetic Map16p11.2UniSTS
Cytogenetic Map12p13.1UniSTS
HuRef1629,140,000 - 29,140,102UniSTS
HuRef1210,580,971 - 10,582,667UniSTS
WI-20104  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371631,579,267 - 31,579,484UniSTSGRCh37
GRCh371210,851,847 - 10,852,067UniSTSGRCh37
Build 361210,743,114 - 10,743,334RGDNCBI36
Celera1628,729,290 - 28,729,507UniSTS
Celera1216,000,171 - 16,000,391RGD
Cytogenetic Map12p13.1UniSTS
Cytogenetic Map16p11.2UniSTS
HuRef1210,580,614 - 10,580,834UniSTS
HuRef1629,139,647 - 29,139,864UniSTS
GeneMap99-GB4 RH Map1253.21UniSTS
Whitehead-RH Map12103.7UniSTS
NCBI RH Map12170.0UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2959
Count of miRNA genes:1007
Interacting mature miRNAs:1215
Transcripts:ENST00000228251, ENST00000279550, ENST00000366286, ENST00000366290, ENST00000536107, ENST00000536823, ENST00000539204, ENST00000540447, ENST00000540747, ENST00000540975, ENST00000541351, ENST00000542002, ENST00000542641, ENST00000544501, ENST00000544504, ENST00000544622, ENST00000546164, ENST00000546298
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.


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 sensory system visual system adipose tissue appendage entire extraembryonic component
High 7 11 1 802 797 802
Medium 2424 2964 1481 384 1897 226 3551 1391 2187 410 1445 1578 171 1204 1986 4
Low 1 12 242 238 31 238 3 7 1509 8 4 23 2
Below cutoff 2 1 17 1 14 1 7 11 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001145426 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_003651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011520871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017020122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017020123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001748906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA621593 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB209896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC021049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH003216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK314846 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AU117252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC008801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC009744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC015564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC015913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC021926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC150580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M24069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X72712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X95325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000228251   ⟹   ENSP00000228251
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,699,089 - 10,723,323 (-)Ensembl
RefSeq Acc Id: ENST00000279550   ⟹   ENSP00000279550
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,699,089 - 10,723,307 (-)Ensembl
RefSeq Acc Id: ENST00000366286
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,699,610 - 10,702,642 (-)Ensembl
RefSeq Acc Id: ENST00000366290
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,701,254 - 10,702,371 (-)Ensembl
RefSeq Acc Id: ENST00000536107
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,717,808 - 10,722,909 (-)Ensembl
RefSeq Acc Id: ENST00000536823
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,699,478 - 10,704,438 (-)Ensembl
RefSeq Acc Id: ENST00000539204
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,704,023 - 10,718,430 (-)Ensembl
RefSeq Acc Id: ENST00000540447
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,699,227 - 10,722,911 (-)Ensembl
RefSeq Acc Id: ENST00000540747
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,718,117 - 10,722,396 (-)Ensembl
RefSeq Acc Id: ENST00000540975
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,699,317 - 10,702,475 (-)Ensembl
RefSeq Acc Id: ENST00000541351
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,701,275 - 10,710,714 (-)Ensembl
RefSeq Acc Id: ENST00000542002
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,701,253 - 10,716,148 (-)Ensembl
RefSeq Acc Id: ENST00000542641
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,701,274 - 10,718,115 (-)Ensembl
RefSeq Acc Id: ENST00000544501
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,715,695 - 10,718,114 (-)Ensembl
RefSeq Acc Id: ENST00000544504
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,702,010 - 10,710,686 (-)Ensembl
RefSeq Acc Id: ENST00000544622   ⟹   ENSP00000485718
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,710,351 - 10,718,121 (-)Ensembl
RefSeq Acc Id: ENST00000546164
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,699,427 - 10,710,120 (-)Ensembl
RefSeq Acc Id: ENST00000546298
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1210,713,229 - 10,722,046 (-)Ensembl
RefSeq Acc Id: NM_001145426   ⟹   NP_001138898
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381210,699,089 - 10,723,323 (-)NCBI
GRCh371210,851,676 - 10,876,047 (-)NCBI
HuRef1210,580,443 - 10,604,713 (-)ENTREZGENE
CHM1_11210,821,053 - 10,845,329 (-)NCBI
Sequence:
RefSeq Acc Id: NM_003651   ⟹   NP_003642
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381210,699,089 - 10,723,323 (-)NCBI
GRCh371210,851,676 - 10,876,047 (-)NCBI
Build 361210,742,955 - 10,767,171 (-)NCBI Archive
HuRef1210,580,443 - 10,604,713 (-)ENTREZGENE
CHM1_11210,821,053 - 10,845,329 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011520871   ⟹   XP_011519173
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381210,710,351 - 10,723,442 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017020122   ⟹   XP_016875611
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381210,699,084 - 10,723,442 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017020123   ⟹   XP_016875612
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381210,699,084 - 10,723,442 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001748906
RefSeq Status:
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381210,699,084 - 10,723,442 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001138898   ⟸   NM_001145426
- Peptide Label: isoform b
- UniProtKB: P16989 (UniProtKB/Swiss-Prot),   A0A024RAV4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_003642   ⟸   NM_003651
- Peptide Label: isoform a
- UniProtKB: P16989 (UniProtKB/Swiss-Prot),   A0A024RAQ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011519173   ⟸   XM_011520871
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_016875612   ⟸   XM_017020123
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_016875611   ⟸   XM_017020122
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSP00000228251   ⟸   ENST00000228251
RefSeq Acc Id: ENSP00000485718   ⟸   ENST00000544622
RefSeq Acc Id: ENSP00000279550   ⟸   ENST00000279550
Protein Domains
CSD   CSD_1   CSP

Promoters
RGD ID:7223191
Promoter ID:EPDNEW_H17342
Type:initiation region
Name:YBX3_1
Description:Y-box binding protein 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381210,723,323 - 10,723,383EPDNEW
RGD ID:6789832
Promoter ID:HG_KWN:15036
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_001145426,   NM_003651
Position:
Human AssemblyChrPosition (strand)Source
Build 361210,766,764 - 10,767,264 (-)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12p13.33-11.22(chr12:121055-28415184)x1 copy number loss See cases [RCV000052776] Chr12:121055..28415184 [GRCh38]
Chr12:282465..28568117 [GRCh37]
Chr12:100482..28459384 [NCBI36]
Chr12:12p13.33-11.22
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:77187-34380176)x3 copy number gain See cases [RCV000053660] Chr12:77187..34380176 [GRCh38]
Chr12:282465..34533111 [GRCh37]
Chr12:56614..34424378 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh38/hg38 12p13.33-12.1(chr12:80412-25470329)x3 copy number gain See cases [RCV000053662] Chr12:80412..25470329 [GRCh38]
Chr12:282465..25623263 [GRCh37]
Chr12:59839..25514530 [NCBI36]
Chr12:12p13.33-12.1
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:212976-33926913)x4 copy number gain See cases [RCV000053666] Chr12:212976..33926913 [GRCh38]
Chr12:322142..34079848 [GRCh37]
Chr12:192403..33971115 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:121255-34603274)x3 copy number gain See cases [RCV000136611] Chr12:121255..34603274 [GRCh38]
Chr12:282465..34756209 [GRCh37]
Chr12:100682..34647476 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh38/hg38 12p13.33-12.3(chr12:2871741-14987348)x3 copy number gain See cases [RCV000137694] Chr12:2871741..14987348 [GRCh38]
Chr12:2980907..15140282 [GRCh37]
Chr12:2851168..15031549 [NCBI36]
Chr12:12p13.33-12.3
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:121271-34603261)x3 copy number gain See cases [RCV000139052] Chr12:121271..34603261 [GRCh38]
Chr12:282465..34756196 [GRCh37]
Chr12:100698..34647463 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:54427-34608071)x4 copy number gain See cases [RCV000139787] Chr12:54427..34608071 [GRCh38]
Chr12:282465..34761006 [GRCh37]
Chr12:33854..34652273 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33
pathogenic
GRCh38/hg38 12p13.33-12.2(chr12:1258274-20657577)x3 copy number gain See cases [RCV000141905] Chr12:1258274..20657577 [GRCh38]
Chr12:1367440..20810511 [GRCh37]
Chr12:1237701..20701778 [NCBI36]
Chr12:12p13.33-12.2
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:64620-34682902)x4 copy number gain See cases [RCV000142149] Chr12:64620..34682902 [GRCh38]
Chr12:173786..34835837 [GRCh37]
Chr12:44047..34727104 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:148034-34178799)x4 copy number gain See cases [RCV000240164] Chr12:148034..34178799 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3 copy number gain See cases [RCV000258805] Chr12:1..133851895 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic|likely pathogenic
chr12:10074776-18800953 complex variant complex Ductal breast carcinoma [RCV000207105] Chr12:10074776..18800953 [GRCh37]
Chr12:12p13.31-12.3
uncertain significance
GRCh37/hg19 12p13.33-11.1(chr12:89061-34178799)x3 copy number gain See cases [RCV000240487] Chr12:89061..34178799 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-q11(chr12:173786-37869301)x3 copy number gain See cases [RCV000449191] Chr12:173786..37869301 [GRCh37]
Chr12:12p13.33-q11
pathogenic
GRCh37/hg19 12p13.33-12.1(chr12:173786-25286865)x3 copy number gain See cases [RCV000449287] Chr12:173786..25286865 [GRCh37]
Chr12:12p13.33-12.1
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x3 copy number gain See cases [RCV000447551] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-12.2(chr12:173786-20026080)x3 copy number gain See cases [RCV000446050] Chr12:173786..20026080 [GRCh37]
Chr12:12p13.33-12.2
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:189578-34756150) copy number gain See cases [RCV000446017] Chr12:189578..34756150 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3 copy number gain See cases [RCV000511580] Chr12:565369..34835837 [GRCh37]
Chr12:12p13.33-11.1
likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902) copy number gain See cases [RCV000511643] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-13.2(chr12:173786-11677456)x3 copy number gain See cases [RCV000510853] Chr12:173786..11677456 [GRCh37]
Chr12:12p13.33-13.2
pathogenic
GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3 copy number gain See cases [RCV000510961] Chr12:173786..28219229 [GRCh37]
Chr12:12p13.33-11.22
pathogenic
GRCh37/hg19 12p13.2-13.1(chr12:10336209-13535349) copy number loss Multiple endocrine neoplasia, type 4 [RCV000767604] Chr12:10336209..13535349 [GRCh37]
Chr12:12p13.2-13.1
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x2,3 copy number gain not provided [RCV000683478] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.2-13.1(chr12:10717428-14032860)x1 copy number loss not provided [RCV000683470] Chr12:10717428..14032860 [GRCh37]
Chr12:12p13.2-13.1
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x3 copy number gain not provided [RCV000683479] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-q11(chr12:173786-37869107)x3 copy number gain not provided [RCV000683480] Chr12:173786..37869107 [GRCh37]
Chr12:12p13.33-q11
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-11.21(chr12:191619-31733044)x3 copy number gain not provided [RCV000750245] Chr12:191619..31733044 [GRCh37]
Chr12:12p13.33-11.21
pathogenic
GRCh37/hg19 12p13.33-12.3(chr12:189216-15001420) copy number gain not provided [RCV000767817] Chr12:189216..15001420 [GRCh37]
Chr12:12p13.33-12.3
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34496628)x3 copy number gain not provided [RCV000847209] Chr12:173786..34496628 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-q11(chr12:274676-37869301)x4 copy number gain not provided [RCV001006470] Chr12:274676..37869301 [GRCh37]
Chr12:12p13.33-q11
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:2428 AgrOrtholog
COSMIC YBX3 COSMIC
Ensembl Genes ENSG00000060138 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000228251 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000279550 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000485718 UniProtKB/TrEMBL
Ensembl Transcript ENST00000228251 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000279550 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000544622 UniProtKB/TrEMBL
GTEx ENSG00000060138 GTEx
HGNC ID HGNC:2428 ENTREZGENE
Human Proteome Map YBX3 Human Proteome Map
InterPro CSD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CSD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CSP_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA-bd_OB-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:8531 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 8531 ENTREZGENE
OMIM 603437 OMIM
Pfam CSD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA26929 PharmGKB
PRINTS COLDSHOCK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CSD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CSD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CSP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50249 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A024RAQ1 ENTREZGENE, UniProtKB/TrEMBL
  A0A024RAV4 ENTREZGENE, UniProtKB/TrEMBL
  A0A0D9SEI8_HUMAN UniProtKB/TrEMBL
  P16989 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary B2RBW6 UniProtKB/Swiss-Prot
  Q14121 UniProtKB/Swiss-Prot
  Q969N6 UniProtKB/Swiss-Prot
  Q96B76 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-24 YBX3  Y-box binding protein 3    Y box binding protein 3  Symbol and/or name change 5135510 APPROVED
2013-03-19 YBX3  Y box binding protein 3  CSDA  cold shock domain protein A  Symbol and/or name change 5135510 APPROVED