EPB41L4A-AS1 (EPB41L4A antisense RNA 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: EPB41L4A-AS1 (EPB41L4A antisense RNA 1) Homo sapiens
Analyze
Symbol: EPB41L4A-AS1
Name: EPB41L4A antisense RNA 1
RGD ID: 2290192
HGNC Page HGNC:30749
Description: INTERACTS WITH (-)-epigallocatechin 3-gallate; 2,2',4,4'-Tetrabromodiphenyl ether; 2-hydroxypropanoic acid
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C5orf26; MGC126893; MGC138282; NCRNA00219; TIGA1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385112,160,526 - 112,162,501 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5112,160,526 - 112,164,818 (+)EnsemblGRCh38hg38GRCh38
GRCh375111,496,223 - 111,498,198 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365111,524,125 - 111,524,816 (+)NCBINCBI36Build 36hg18NCBI36
Celera5107,441,942 - 107,443,917 (+)NCBICelera
Cytogenetic Map5q22.1NCBI
HuRef5106,675,408 - 106,677,383 (+)NCBIHuRef
CHM1_15110,929,460 - 110,931,434 (+)NCBICHM1_1
T2T-CHM13v2.05112,670,980 - 112,672,955 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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:9490301   PMID:12477932   PMID:15489334   PMID:15994437   PMID:16344560   PMID:16973895   PMID:27980086   PMID:29117863   PMID:30796006   PMID:31612476   PMID:32557646   PMID:35181612  
PMID:36734855   PMID:37024023  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q21.3-23.1(chr5:108585264-116815075)x1 copy number loss See cases [RCV000133813] Chr5:108585264..116815075 [GRCh38]
Chr5:107920965..116150771 [GRCh37]
Chr5:107948864..116178670 [NCBI36]
Chr5:5q21.3-23.1		 pathogenic
GRCh38/hg38 5q21.3-23.1(chr5:107002209-118025316)x1 copy number loss See cases [RCV000135699] Chr5:107002209..118025316 [GRCh38]
Chr5:106337910..117361011 [GRCh37]
Chr5:106365809..117388910 [NCBI36]
Chr5:5q21.3-23.1		 pathogenic
GRCh38/hg38 5q22.1-23.2(chr5:111463016-127193038)x1 copy number loss See cases [RCV000135549] Chr5:111463016..127193038 [GRCh38]
Chr5:110798714..126528730 [GRCh37]
Chr5:110826613..126556629 [NCBI36]
Chr5:5q22.1-23.2		 pathogenic
GRCh38/hg38 5q22.1-23.3(chr5:110687442-130103838)x1 copy number loss See cases [RCV000139235] Chr5:110687442..130103838 [GRCh38]
Chr5:110023143..129439531 [GRCh37]
Chr5:110051042..129467430 [NCBI36]
Chr5:5q22.1-23.3		 pathogenic|uncertain significance
GRCh38/hg38 5q14.3-23.3(chr5:90374606-128076423)x1 copy number loss See cases [RCV000139893] Chr5:90374606..128076423 [GRCh38]
Chr5:89670423..127412115 [GRCh37]
Chr5:89706179..127440014 [NCBI36]
Chr5:5q14.3-23.3		 pathogenic
GRCh38/hg38 5q14.3-23.1(chr5:92899734-119614119)x1 copy number loss See cases [RCV000141252] Chr5:92899734..119614119 [GRCh38]
Chr5:92235441..118949814 [GRCh37]
Chr5:92261197..118977713 [NCBI36]
Chr5:5q14.3-23.1		 pathogenic
GRCh38/hg38 5q21.3-22.2(chr5:106586078-113006585)x1 copy number loss See cases [RCV000142171] Chr5:106586078..113006585 [GRCh38]
Chr5:105921779..112342282 [GRCh37]
Chr5:105949678..112370181 [NCBI36]
Chr5:5q21.3-22.2		 pathogenic
GRCh38/hg38 5q21.3-23.2(chr5:108308463-125777797)x1 copy number loss See cases [RCV000143326] Chr5:108308463..125777797 [GRCh38]
Chr5:107644164..125113490 [GRCh37]
Chr5:107672063..125141389 [NCBI36]
Chr5:5q21.3-23.2		 pathogenic
GRCh38/hg38 5q15-22.2(chr5:93193104-113287795)x1 copy number loss See cases [RCV000143249] Chr5:93193104..113287795 [GRCh38]
Chr5:92528810..112623492 [GRCh37]
Chr5:92554566..112651391 [NCBI36]
Chr5:5q15-22.2		 pathogenic
GRCh38/hg38 5q14.3-31.1(chr5:91411708-131319563)x1 copy number loss See cases [RCV000143746] Chr5:91411708..131319563 [GRCh38]
Chr5:90707525..130655256 [GRCh37]
Chr5:90743281..130683155 [NCBI36]
Chr5:5q14.3-31.1		 pathogenic
GRCh38/hg38 5q15-22.3(chr5:96454445-114050905)x3 copy number gain See cases [RCV000051841] Chr5:96454445..114050905 [GRCh38]
Chr5:95790149..113386602 [GRCh37]
Chr5:95815905..113414501 [NCBI36]
Chr5:5q15-22.3		 pathogenic
GRCh38/hg38 5q22.1-22.2(chr5:112161743-112421091)x1 copy number loss See cases [RCV000052577] Chr5:112161743..112421091 [GRCh38]
Chr5:111497440..111756788 [GRCh37]
Chr5:111525339..111784687 [NCBI36]
Chr5:5q22.1-22.2		 uncertain significance
GRCh38/hg38 5q21.1-22.2(chr5:102373396-113594030)x1 copy number loss See cases [RCV000053523] Chr5:102373396..113594030 [GRCh38]
Chr5:101709100..112929727 [GRCh37]
Chr5:101736999..112957626 [NCBI36]
Chr5:5q21.1-22.2		 pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:620
Count of miRNA genes:368
Interacting mature miRNAs:398
Transcripts:ENST00000413221, ENST00000427306, ENST00000442823, ENST00000508590
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.

Markers in Region
SGC33358  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375111,497,843 - 111,497,992UniSTSGRCh37
Build 365111,525,742 - 111,525,891RGDNCBI36
Celera5107,443,562 - 107,443,711RGD
Cytogenetic Map5q22.2UniSTS
Cytogenetic Map5q21.3UniSTS
HuRef5106,677,028 - 106,677,177UniSTS
GeneMap99-GB4 RH Map5470.24UniSTS
Whitehead-RH Map5376.6UniSTS
NCBI RH Map5781.8UniSTS
SGC31219  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375111,498,347 - 111,498,472UniSTSGRCh37
Build 365111,526,246 - 111,526,371RGDNCBI36
Celera5107,444,066 - 107,444,191RGD
Cytogenetic Map5q22.2UniSTS
Cytogenetic Map5q21.3UniSTS
HuRef5106,677,532 - 106,677,657UniSTS
TNG Radiation Hybrid Map549913.0UniSTS
GeneMap99-GB4 RH Map5469.12UniSTS
Whitehead-RH Map5374.3UniSTS
UniSTS:485944  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375111,496,226 - 111,496,917UniSTSGRCh37
Celera5107,441,945 - 107,442,636UniSTS
HuRef5106,675,411 - 106,676,102UniSTS


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
Medium 2361 1750 1321 249 1326 91 3895 1354 3591 307 1389 1485 165 1201 2374 3
Low 75 1236 404 375 621 373 462 839 131 111 62 126 7 1 3 414 1 2
Below cutoff 2 3 2 1 9 1 8 1 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000413221
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5112,160,872 - 112,164,257 (+)Ensembl
RefSeq Acc Id: ENST00000427306
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5112,160,529 - 112,162,315 (+)Ensembl
RefSeq Acc Id: ENST00000442823
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5112,160,865 - 112,162,324 (+)Ensembl
RefSeq Acc Id: ENST00000508590
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5112,160,864 - 112,162,315 (+)Ensembl
RefSeq Acc Id: ENST00000663232
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5112,160,526 - 112,164,818 (+)Ensembl
RefSeq Acc Id: ENST00000688370
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5112,160,864 - 112,162,310 (+)Ensembl
RefSeq Acc Id: ENST00000690733
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5112,160,865 - 112,162,315 (+)Ensembl
RefSeq Acc Id: ENST00000702181
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5112,160,860 - 112,162,312 (+)Ensembl
RefSeq Acc Id: ENST00000702686
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5112,160,901 - 112,162,312 (+)Ensembl
RefSeq Acc Id: NR_015370
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385112,160,526 - 112,162,501 (+)NCBI
GRCh375111,496,223 - 111,498,198 (+)RGD
Celera5107,441,942 - 107,443,917 (+)RGD
HuRef5106,675,408 - 106,677,383 (+)ENTREZGENE
CHM1_15110,929,460 - 110,931,434 (+)NCBI
T2T-CHM13v2.05112,670,980 - 112,672,955 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein BAB64313 (Get FASTA)   NCBI Sequence Viewer  
  EAW49016 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:6802925
Promoter ID:HG_KWN:50820
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:NR_015370,   OTTHUMT00000313610,   UC003KPQ.1
Position:
Human AssemblyChrPosition (strand)Source
Build 365111,524,216 - 111,524,716 (+)MPROMDB
RGD ID:15095933
Promoter ID:EPDNEWNC_H770
Type:multiple initiation site
Name:EPB41L4A-AS1_1
Description:EPB41L4A antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:30749]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh385112,160,865 - 112,160,925EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC EPB41L4A-AS1 COSMIC
Ensembl Genes ENSG00000224032 Ensembl
GTEx ENSG00000224032 GTEx
HGNC ID HGNC:30749 ENTREZGENE
Human Proteome Map EPB41L4A-AS1 Human Proteome Map
NCBI Gene 114915 ENTREZGENE
PharmGKB PA165660388 PharmGKB
RNAcentral URS000075CCBD RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-21 EPB41L4A-AS1  EPB41L4A antisense RNA 1  EPB41L4A-AS1  EPB41L4A antisense RNA 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED
2011-09-01 EPB41L4A-AS1  EPB41L4A antisense RNA 1 (non-protein coding)  NCRNA00219  non-protein coding RNA 219  Symbol and/or name change 5135510 APPROVED
2011-07-27 NCRNA00219  non-protein coding RNA 219  C5orf26  chromosome 5 open reading frame 26  Symbol and/or name change 5135510 APPROVED