ATXN7L3B (ataxin 7 like 3B) - Rat Genome Database

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Gene: ATXN7L3B (ataxin 7 like 3B) Homo sapiens
Analyze
Symbol: ATXN7L3B
Name: ataxin 7 like 3B
RGD ID: 2816966
HGNC Page HGNC:37931
Description: Involved in regulation of gene expression. Located in cytoplasm.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: #8203; ataxin 7-like 3B; ataxin-7-like protein 3B; FLJ32080; lnc-SCA7; MGC17296; putative ataxin-7-like protein 3B
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381274,537,835 - 74,545,430 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1274,537,835 - 74,545,430 (+)EnsemblGRCh38hg38GRCh38
GRCh371274,931,615 - 74,939,210 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361273,217,818 - 73,221,499 (+)NCBINCBI36Build 36hg18NCBI36
Celera1274,598,676 - 74,602,356 (+)NCBICelera
Cytogenetic Map12q21.1NCBI
HuRef1271,980,617 - 71,984,292 (+)NCBIHuRef
CHM1_11274,896,842 - 74,900,522 (+)NCBICHM1_1
T2T-CHM13v2.01274,511,693 - 74,519,285 (+)NCBIT2T-CHM13v2.0
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
cytoplasm  (IDA,IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:16344560   PMID:19615732   PMID:21873635   PMID:23475819   PMID:24797263   PMID:25306109   PMID:27432908   PMID:27601583   PMID:29117863   PMID:31091453  
PMID:31797724   PMID:32202298   PMID:34375763   PMID:35271311   PMID:35831314  


Genomics

Comparative Map Data
ATXN7L3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381274,537,835 - 74,545,430 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1274,537,835 - 74,545,430 (+)EnsemblGRCh38hg38GRCh38
GRCh371274,931,615 - 74,939,210 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361273,217,818 - 73,221,499 (+)NCBINCBI36Build 36hg18NCBI36
Celera1274,598,676 - 74,602,356 (+)NCBICelera
Cytogenetic Map12q21.1NCBI
HuRef1271,980,617 - 71,984,292 (+)NCBIHuRef
CHM1_11274,896,842 - 74,900,522 (+)NCBICHM1_1
T2T-CHM13v2.01274,511,693 - 74,519,285 (+)NCBIT2T-CHM13v2.0
Atxn7l3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910112,761,333 - 112,764,931 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10112,761,335 - 112,764,906 (-)EnsemblGRCm39 Ensembl
GRCm3810112,925,428 - 112,929,026 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10112,925,430 - 112,929,001 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710112,362,484 - 112,366,082 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610112,332,611 - 112,335,265 (+)NCBIMGSCv36mm8
Celera10114,851,808 - 114,855,406 (-)NCBICelera
Cytogenetic Map10D2NCBI
cM Map1060.92NCBI
Atxn7l3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8750,208,666 - 50,212,190 (-)NCBIGRCr8
mRatBN7.2748,322,451 - 48,325,975 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl748,321,755 - 48,328,878 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx750,234,597 - 50,238,121 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0752,437,708 - 52,441,232 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0752,215,520 - 52,219,044 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0755,600,879 - 55,604,403 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl755,600,889 - 55,604,403 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0755,621,384 - 55,624,908 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4751,875,726 - 51,879,250 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera745,121,840 - 45,125,364 (-)NCBICelera
Cytogenetic Map7q22NCBI
Atxn7l3b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540514,094,074 - 14,094,367 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540514,093,770 - 14,097,409 (+)NCBIChiLan1.0ChiLan1.0
ATXN7L3B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21082,587,628 - 82,591,305 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11282,584,063 - 82,587,702 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01272,072,195 - 72,075,869 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11274,925,659 - 74,929,346 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1274,925,995 - 74,926,288 (+)Ensemblpanpan1.1panPan2
ATXN7L3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11015,361,259 - 15,363,931 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1015,294,655 - 15,298,597 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01015,531,125 - 15,535,058 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1015,531,194 - 15,531,487 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11015,357,608 - 15,361,542 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01015,606,764 - 15,610,704 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01015,734,423 - 15,738,358 (+)NCBIUU_Cfam_GSD_1.0
Atxn7l3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494542,625,821 - 42,629,454 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365683,099,190 - 3,099,483 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365683,098,877 - 3,102,499 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATXN7L3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl537,978,739 - 37,982,422 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1537,978,712 - 37,982,432 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2541,166,741 - 41,170,460 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATXN7L3B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11170,106,011 - 70,109,699 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1170,106,348 - 70,106,638 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037175,436,749 - 175,440,443 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Atxn7l3b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475023,381,494 - 23,381,787 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475023,378,545 - 23,382,111 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in ATXN7L3B
5 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12q15-21.31(chr12:70337484-81761145)x1 copy number loss See cases [RCV000051313] Chr12:70337484..81761145 [GRCh38]
Chr12:70731264..82154924 [GRCh37]
Chr12:69017531..80679055 [NCBI36]
Chr12:12q15-21.31		 pathogenic
GRCh38/hg38 12q15-21.2(chr12:70390897-79214318)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051314]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051314]|See cases [RCV000051314] Chr12:70390897..79214318 [GRCh38]
Chr12:70784677..79608098 [GRCh37]
Chr12:69070944..78132229 [NCBI36]
Chr12:12q15-21.2		 pathogenic
GRCh38/hg38 12q15-21.2(chr12:68011417-75383054)x1 copy number loss See cases [RCV000135587] Chr12:68011417..75383054 [GRCh38]
Chr12:68405197..75776834 [GRCh37]
Chr12:66691464..74063101 [NCBI36]
Chr12:12q15-21.2		 likely pathogenic|uncertain significance
GRCh38/hg38 12q15-21.2(chr12:69769737-76964217)x1 copy number loss See cases [RCV000136267] Chr12:69769737..76964217 [GRCh38]
Chr12:70163517..77357997 [GRCh37]
Chr12:68449784..75882128 [NCBI36]
Chr12:12q15-21.2		 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 12q21.1-22(chr12:73485697-92795805)x1 copy number loss See cases [RCV000143099] Chr12:73485697..92795805 [GRCh38]
Chr12:73879477..93189581 [GRCh37]
Chr12:72165744..91713712 [NCBI36]
Chr12:12q21.1-22		 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
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-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-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-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12q15-21.33(chr12:69608090-89629345)x1 copy number loss not provided [RCV000737927] Chr12:69608090..89629345 [GRCh37]
Chr12:12q15-21.33		 pathogenic
GRCh37/hg19 12q14.3-21.1(chr12:65251705-75263379)x1 copy number loss not provided [RCV001537907] Chr12:65251705..75263379 [GRCh37]
Chr12:12q14.3-21.1		 pathogenic
GRCh37/hg19 12q15-21.2(chr12:70084476-77065764)x1 copy number loss not provided [RCV001834178] Chr12:70084476..77065764 [GRCh37]
Chr12:12q15-21.2		 pathogenic
NM_001136262.2(ATXN7L3B):c.251G>A (p.Gly84Glu) single nucleotide variant Inborn genetic diseases [RCV002645168] Chr12:74538363 [GRCh38]
Chr12:74932143 [GRCh37]
Chr12:12q21.1		 uncertain significance
NM_001136262.2(ATXN7L3B):c.250G>A (p.Gly84Arg) single nucleotide variant Inborn genetic diseases [RCV002649233] Chr12:74538362 [GRCh38]
Chr12:74932142 [GRCh37]
Chr12:12q21.1		 uncertain significance
NM_001136262.2(ATXN7L3B):c.211C>T (p.Arg71Cys) single nucleotide variant Inborn genetic diseases [RCV003214611] Chr12:74538323 [GRCh38]
Chr12:74932103 [GRCh37]
Chr12:12q21.1		 uncertain significance
NM_001136262.2(ATXN7L3B):c.271C>T (p.Arg91Cys) single nucleotide variant Inborn genetic diseases [RCV003383531] Chr12:74538383 [GRCh38]
Chr12:74932163 [GRCh37]
Chr12:12q21.1		 uncertain significance
GRCh37/hg19 12q21.1(chr12:74931615-75445097)x1 copy number loss not provided [RCV003398323] Chr12:74931615..75445097 [GRCh37]
Chr12:12q21.1		 uncertain significance
GRCh37/hg19 12q21.1-21.33(chr12:74887087-90469800)x1 copy number loss not specified [RCV003986972] Chr12:74887087..90469800 [GRCh37]
Chr12:12q21.1-21.33		 pathogenic
GRCh37/hg19 12q21.1-21.31(chr12:73466055-82398026)x1 copy number loss not specified [RCV003986983] Chr12:73466055..82398026 [GRCh37]
Chr12:12q21.1-21.31		 uncertain significance
GRCh37/hg19 12q21.1(chr12:74449382-75057687)x1 copy number loss not specified [RCV003986965] Chr12:74449382..75057687 [GRCh37]
Chr12:12q21.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1249
Count of miRNA genes:779
Interacting mature miRNAs:883
Transcripts:ENST00000519948
Prediction methods:Miranda
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.

Markers in Region
IB3090  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371274,934,883 - 74,935,202UniSTSGRCh37
Build 361273,221,150 - 73,221,469RGDNCBI36
Celera1274,602,007 - 74,602,326RGD
Cytogenetic Map12q21UniSTS
HuRef1271,983,944 - 71,984,262UniSTS
GeneMap99-GB4 RH Map12309.34UniSTS
Whitehead-RH Map12405.3UniSTS
NCBI RH Map12548.5UniSTS
D12S1191E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371274,934,991 - 74,935,186UniSTSGRCh37
Build 361273,221,258 - 73,221,453RGDNCBI36
Celera1274,602,115 - 74,602,310RGD
Cytogenetic Map12q21UniSTS
HuRef1271,984,051 - 71,984,246UniSTS
GeneMap99-GB4 RH Map12307.22UniSTS
NCBI RH Map12548.5UniSTS
1798  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371274,934,103 - 74,934,190UniSTSGRCh37
Build 361273,220,370 - 73,220,457RGDNCBI36
Celera1274,601,227 - 74,601,314RGD
Cytogenetic Map12q21UniSTS
HuRef1271,983,164 - 71,983,251UniSTS
GeneMap99-GB4 RH Map12309.44UniSTS
NCBI RH Map12548.5UniSTS
D12S1415  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371274,934,974 - 74,935,206UniSTSGRCh37
Build 361273,221,241 - 73,221,473RGDNCBI36
Celera1274,602,098 - 74,602,330RGD
Cytogenetic Map12q21UniSTS
HuRef1271,984,034 - 71,984,266UniSTS
Whitehead-YAC Contig Map12 UniSTS


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 pharyngeal arch
High 1
Medium 2408 2029 1613 523 1383 365 4230 1829 3509 400 1426 1607 171 1186 2668 4
Low 30 960 113 101 564 100 126 367 218 18 29 6 4 1 18 120 2 2
Below cutoff 1 2 6 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000519948   ⟹   ENSP00000430000
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1274,537,835 - 74,545,430 (+)Ensembl
RefSeq Acc Id: NM_001136262   ⟹   NP_001129734
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381274,537,835 - 74,545,430 (+)NCBI
GRCh371274,931,551 - 74,935,232 (+)RGD
Celera1274,598,676 - 74,602,356 (+)RGD
HuRef1271,980,617 - 71,984,292 (+)ENTREZGENE
CHM1_11274,896,842 - 74,900,522 (+)NCBI
T2T-CHM13v2.01274,511,693 - 74,519,285 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001129734 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH09111 (Get FASTA)   NCBI Sequence Viewer  
  EAW97284 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000430000
  ENSP00000430000.2
GenBank Protein Q96GX2 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001129734   ⟸   NM_001136262
- UniProtKB: Q96GX2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000430000   ⟸   ENST00000519948

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q96GX2-F1-model_v2 AlphaFold Q96GX2 1-97 view protein structure

Promoters
RGD ID:6789693
Promoter ID:HG_KWN:16172
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000315355,   NM_001136262
Position:
Human AssemblyChrPosition (strand)Source
Build 361273,217,871 - 73,218,757 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:37931 AgrOrtholog
COSMIC ATXN7L3B COSMIC
Ensembl Genes ENSG00000253719 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000519948 ENTREZGENE
  ENST00000519948.4 UniProtKB/Swiss-Prot
GTEx ENSG00000253719 GTEx
HGNC ID HGNC:37931 ENTREZGENE
Human Proteome Map ATXN7L3B Human Proteome Map
InterPro ATXN7L3B UniProtKB/Swiss-Prot
KEGG Report hsa:552889 UniProtKB/Swiss-Prot
NCBI Gene 552889 ENTREZGENE
OMIM 615579 OMIM
PANTHER ATAXIN-7-LIKE PROTEIN 3B UniProtKB/Swiss-Prot
  PTHR47733 UniProtKB/Swiss-Prot
PharmGKB PA165512339 PharmGKB
UniProt A7L3B_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-26 ATXN7L3B  ataxin 7 like 3B    ataxin 7-like 3B  Symbol and/or name change 5135510 APPROVED