GASAL1 (growth arrest associated lncRNA 1) - Rat Genome Database

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Gene: GASAL1 (growth arrest associated lncRNA 1) Homo sapiens
Analyze
Symbol: GASAL1
Name: growth arrest associated lncRNA 1
RGD ID: 11231739
HGNC Page HGNC
Description:
Type: ncrna
RefSeq Status: VALIDATED
Also known as: GASL1; LOC401472; myosin IC heavy chain; uncharacterized LOC401472
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8102,805,517 - 102,810,039 (+)EnsemblGRCh38hg38GRCh38
GRCh388102,806,822 - 102,811,214 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378103,819,050 - 103,823,442 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera8100,006,235 - 100,007,003 (+)NCBI
Cytogenetic Map8q22.3NCBI
HuRef899,020,071 - 99,020,839 (+)NCBIHuRef
CHM1_18103,859,332 - 103,862,301 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:28423601   PMID:30468472   PMID:30742604   PMID:31223316  


Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:351
Count of miRNA genes:322
Interacting mature miRNAs:341
Transcripts:ENST00000517910, ENST00000522715
Prediction methods: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.


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 adipose tissue appendage entire extraembryonic component
High
Medium 8 2 2 6 2 5 7 1 1 8 4
Low 881 704 1126 291 1060 276 1626 458 538 231 886 1141 28 661 782 3
Below cutoff 1536 2239 595 329 851 187 2676 1710 3144 185 554 459 143 539 1977 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_149020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AP003356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000517910
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8102,806,822 - 102,809,971 (+)Ensembl
RefSeq Acc Id: ENST00000522715
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8102,805,517 - 102,809,566 (+)Ensembl
RefSeq Acc Id: ENST00000663613
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8102,807,741 - 102,810,039 (+)Ensembl
RefSeq Acc Id: ENST00000665815
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8102,808,535 - 102,810,039 (+)Ensembl
RefSeq Acc Id: ENST00000670970
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8102,807,674 - 102,810,035 (+)Ensembl
RefSeq Acc Id: NR_149020
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388102,806,822 - 102,811,214 (+)NCBI
Sequence:
Promoters
RGD ID:15096252
Promoter ID:EPDNEWNC_H1079
Type:initiation region
Name:GASAL1_1
Description:growth arrest associated lncRNA 1 [Source:HGNCSymbol;Acc:HGNC:53461]
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
GRCh388102,806,784 - 102,806,844EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 8q22.3(chr8:101962098-103357772)x3 copy number gain See cases [RCV000050760] Chr8:101962098..103357772 [GRCh38]
Chr8:102974326..104370000 [GRCh37]
Chr8:103043502..104439176 [NCBI36]
Chr8:8q22.3
pathogenic
GRCh38/hg38 8q22.3-23.1(chr8:101884819-107356143)x1 copy number loss See cases [RCV000134099] Chr8:101884819..107356143 [GRCh38]
Chr8:102897047..108368371 [GRCh37]
Chr8:102966223..108437547 [NCBI36]
Chr8:8q22.3-23.1
pathogenic
GRCh38/hg38 8q22.3-23.1(chr8:101199826-105802098)x1 copy number loss See cases [RCV000136812] Chr8:101199826..105802098 [GRCh38]
Chr8:102212054..106814326 [GRCh37]
Chr8:102281230..106883502 [NCBI36]
Chr8:8q22.3-23.1
pathogenic
GRCh38/hg38 8q22.3-23.1(chr8:101171263-109127664)x1 copy number loss See cases [RCV000138134] Chr8:101171263..109127664 [GRCh38]
Chr8:102183491..110139893 [GRCh37]
Chr8:102252667..110209069 [NCBI36]
Chr8:8q22.3-23.1
pathogenic
GRCh38/hg38 8q22.2-23.1(chr8:100179408-106524667)x1 copy number loss See cases [RCV000141697] Chr8:100179408..106524667 [GRCh38]
Chr8:101191636..107536895 [GRCh37]
Chr8:101260812..107606071 [NCBI36]
Chr8:8q22.2-23.1
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:244417-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|See cases [RCV000053604] Chr8:244417..145054775 [GRCh38]
Chr8:194417..146280161 [GRCh37]
Chr8:184417..146250965 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:95606052-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|See cases [RCV000053677] Chr8:95606052..145054775 [GRCh38]
Chr8:96618280..146280161 [GRCh37]
Chr8:96687456..146250965 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:94682154-145068656)x3 copy number gain See cases [RCV000134353] Chr8:94682154..145068656 [GRCh38]
Chr8:95694382..146294042 [GRCh37]
Chr8:95763558..146264846 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q21.3-24.3(chr8:87931152-145068712)x3 copy number gain See cases [RCV000138551] Chr8:87931152..145068712 [GRCh38]
Chr8:88943380..146294098 [GRCh37]
Chr8:89012496..146264902 [NCBI36]
Chr8:8q21.3-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:77480050-145068712)x3 copy number gain See cases [RCV000139036] Chr8:77480050..145068712 [GRCh38]
Chr8:78392286..146294098 [GRCh37]
Chr8:78554841..146264902 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8q11.1-24.3(chr8:46031340-139285494)x3 copy number gain See cases [RCV000139539] Chr8:46031340..139285494 [GRCh38]
Chr8:46942962..140297737 [GRCh37]
Chr8:47062127..140366919 [NCBI36]
Chr8:8q11.1-24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:97382873-145070385)x3 copy number gain See cases [RCV000140447] Chr8:97382873..145070385 [GRCh38]
Chr8:98395101..146295771 [GRCh37]
Chr8:98464277..146266575 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:100867343-145070385)x3 copy number gain See cases [RCV000141694] Chr8:100867343..145070385 [GRCh38]
Chr8:101879571..146295771 [GRCh37]
Chr8:101948747..146266575 [NCBI36]
Chr8:8q22.3-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:78614077-145054634)x3 copy number gain See cases [RCV000142597] Chr8:78614077..145054634 [GRCh38]
Chr8:79526312..146280020 [GRCh37]
Chr8:79688867..146250824 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.2-24.3(chr8:85765999-145070385)x3 copy number gain See cases [RCV000143659] Chr8:85765999..145070385 [GRCh38]
Chr8:86778228..146295771 [GRCh37]
Chr8:86863079..146266575 [NCBI36]
Chr8:8q21.2-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000148092] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.3-24.23(chr8:86300584-137022587)x3 copy number gain See cases [RCV000135621] Chr8:86300584..137022587 [GRCh38]
Chr8:87312813..138034830 [GRCh37]
Chr8:87381929..138104012 [NCBI36]
Chr8:8q21.3-24.23
pathogenic|likely pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC GASAL1 COSMIC
Ensembl Genes ENSG00000253669 Ensembl
GTEx ENSG00000253669 GTEx
HGNC ID HGNC:53461 ENTREZGENE
Human Proteome Map GASAL1 Human Proteome Map
NCBI Gene LOC401472 ENTREZGENE
RNAcentral URS0000BC44C1 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-11-21 GASAL1  growth arrest associated lncRNA 1  GASAL1  growth arrest associated lncRNA 1  Data Merged 737654 PROVISIONAL
2017-09-05 GASAL1  growth arrest associated lncRNA 1  LOC401472  uncharacterized LOC401472  Symbol and/or name change 5135510 APPROVED
2017-08-29 LOC401472  uncharacterized LOC401472    myosin IC heavy chain  Symbol and/or name change 5135510 APPROVED