GACAT1 (gastric cancer associated transcript 1) - Rat Genome Database
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Gene: GACAT1 (gastric cancer associated transcript 1) Homo sapiens
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Symbol: GACAT1
Name: gastric cancer associated transcript 1
RGD ID: 9588902
HGNC Page HGNC
Description: ASSOCIATED WITH schizophrenia; INTERACTS WITH aflatoxin B1
Type: ncrna
RefSeq Status: VALIDATED
Also known as: gastric cancer associated transcript 1 (non-protein coding); LINC00876
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2107,754,112 - 107,822,129 (+)EnsemblGRCh38hg38GRCh38
GRCh382107,754,112 - 107,822,129 (+)NCBIGRCh38GRCh38hg38GRCh38
Cytogenetic Map2q12.3NCBI
CHM1_12108,374,983 - 108,442,979 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
schizophrenia  (IAGP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
aflatoxin B1  (EXP)

References
Additional References at PubMed
PMID:16344560   PMID:23645148   PMID:24833871  


Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:226
Count of miRNA genes:212
Interacting mature miRNAs:217
Transcripts:ENST00000419650, ENST00000441383
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.


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 adipose tissue appendage
High
Medium
Low 2 1 2 1 4 1 3 97 1
Below cutoff 19 63 24 4 36 4 40 21 28 16 293 39 11 21

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000419650
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,754,145 - 107,812,348 (+)Ensembl
RefSeq Acc Id: ENST00000441383
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,754,112 - 107,822,129 (+)Ensembl
RefSeq Acc Id: NR_126369
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382107,754,112 - 107,812,348 (+)NCBI
CHM1_12108,374,983 - 108,433,200 (+)NCBI
Sequence:
RefSeq Acc Id: NR_126370
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382107,754,112 - 107,822,129 (+)NCBI
CHM1_12108,374,983 - 108,442,979 (+)NCBI
Sequence:

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_126369.1(GACAT1):n.278+15072T>C single nucleotide variant Lung cancer [RCV000091130] Chr2:107770672 [GRCh38]
Chr2:108387128 [GRCh37]
Chr2:2q12.3
uncertain significance
NR_126369.1(GACAT1):n.279-8571C>G single nucleotide variant Lung cancer [RCV000091131] Chr2:107802109 [GRCh38]
Chr2:108418565 [GRCh37]
Chr2:2q12.3
uncertain significance
GRCh38/hg38 2q12.2-13(chr2:106516472-110576905)x3 copy number gain See cases [RCV000139569] Chr2:106516472..110576905 [GRCh38]
Chr2:107132928..111334482 [GRCh37]
Chr2:106499360..110857227 [NCBI36]
Chr2:2q12.2-13
uncertain significance
GRCh38/hg38 2q12.2-14.1(chr2:106428663-112379067)x3 copy number gain See cases [RCV000140834] Chr2:106428663..112379067 [GRCh38]
Chr2:107045119..113136644 [GRCh37]
Chr2:106411551..112853115 [NCBI36]
Chr2:2q12.2-14.1
uncertain significance
GRCh38/hg38 2q11.1-13(chr2:94678532-110602409)x3 copy number gain See cases [RCV000141075] Chr2:94678532..110602409 [GRCh38]
Chr2:95344257..111359986 [GRCh37]
Chr2:94707984..111076455 [NCBI36]
Chr2:2q11.1-13
pathogenic
GRCh38/hg38 2q11.2-13(chr2:101710825-110791418)x3 copy number gain See cases [RCV000138645] Chr2:101710825..110791418 [GRCh38]
Chr2:102327287..111548995 [GRCh37]
Chr2:101693719..111265466 [NCBI36]
Chr2:2q11.2-13
pathogenic
GRCh38/hg38 2q11.2-13(chr2:97672522-110211318)x3 copy number gain See cases [RCV000052947] Chr2:97672522..110211318 [GRCh38]
Chr2:98288985..110968895 [GRCh37]
Chr2:97655417..110326184 [NCBI36]
Chr2:2q11.2-13
pathogenic
GRCh38/hg38 2q12.2-13(chr2:106696282-110223328)x3 copy number gain See cases [RCV000053141] Chr2:106696282..110223328 [GRCh38]
Chr2:107312738..110980905 [GRCh37]
Chr2:106679170..110338194 [NCBI36]
Chr2:2q12.2-13
uncertain significance
GRCh38/hg38 2q11.2-12.3(chr2:100378510-108472871)x3 copy number gain See cases [RCV000050836] Chr2:100378510..108472871 [GRCh38]
Chr2:100994972..109089327 [GRCh37]
Chr2:100361404..108455759 [NCBI36]
Chr2:2q11.2-12.3
pathogenic
GRCh38/hg38 2q12.2-12.3(chr2:106260759-107904531)x1 copy number loss See cases [RCV000051289] Chr2:106260759..107904531 [GRCh38]
Chr2:106877215..108520987 [GRCh37]
Chr2:106243647..107887419 [NCBI36]
Chr2:2q12.2-12.3
uncertain significance
GRCh38/hg38 2q12.2-12.3(chr2:106261594-107786796)x1 copy number loss See cases [RCV000051290] Chr2:106261594..107786796 [GRCh38]
Chr2:106878050..108403252 [GRCh37]
Chr2:106244482..107769684 [NCBI36]
Chr2:2q12.2-12.3
uncertain significance
GRCh38/hg38 2q12.2-12.3(chr2:105828398-108080417)x3 copy number gain See cases [RCV000052691] Chr2:105828398..108080417 [GRCh38]
Chr2:106444854..108696873 [GRCh37]
Chr2:105811286..108063305 [NCBI36]
Chr2:2q12.2-12.3
uncertain significance
NC_000002.12:g.(?_106480385)_(107825992_?)del deletion Schizophrenia [RCV000416711] Chr2:106480385..107825992 [GRCh38]
Chr2:107096841..108442448 [GRCh37]
Chr2:106463273..107808880 [NCBI36]
Chr2:2q12.2-12.3
likely pathogenic
NC_000002.12:g.(?_106287425)_(107812162_?)dup duplication Schizophrenia [RCV000416938] Chr2:106287425..107812162 [GRCh38]
Chr2:106903881..108428618 [GRCh37]
Chr2:106270313..107795050 [NCBI36]
Chr2:2q12.2-12.3
likely pathogenic
Single allele deletion not provided [RCV000677995] Chr2:106312802..107890728 [GRCh38]
Chr2:106929257..108507183 [GRCh37]
Chr2:2q12.2-12.3
uncertain significance
NC_000002.12:g.(?_106445028)_(107839483_?)del deletion Schizophrenia [RCV000754224] Chr2:106445028..107839483 [GRCh38]
Chr2:2q12.2-12.3
likely pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC GACAT1 COSMIC
Ensembl Genes ENSG00000232991 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000419650 ENTREZGENE
  ENST00000441383 ENTREZGENE
GTEx ENSG00000232991 GTEx
HGNC ID HGNC:48336 ENTREZGENE
Human Proteome Map GACAT1 Human Proteome Map
NCBI Gene GACAT1 ENTREZGENE
RNAcentral URS00000063DA RNACentral
  URS00007E3549 RNACentral
UniGene Hs.585967 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 GACAT1  gastric cancer associated transcript 1    gastric cancer associated transcript 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED