HCCAT5 (hepatocellular carcinoma associated transcript 5) - Rat Genome Database

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Gene: HCCAT5 (hepatocellular carcinoma associated transcript 5) Homo sapiens
Analyze
Symbol: HCCAT5
Name: hepatocellular carcinoma associated transcript 5
RGD ID: 7244818
HGNC Page HGNC:48612
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: FJ222407; hepatocellular carcinoma associated transcript 5 (non-protein coding); HTA; RP11-346C20.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381673,092,349 - 73,093,774 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1673,092,349 - 73,099,337 (+)EnsemblGRCh38hg38GRCh38
GRCh371673,126,248 - 73,127,673 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361671,684,025 - 71,685,174 (+)NCBINCBI36Build 36hg18NCBI36
Celera1657,440,789 - 57,442,214 (+)NCBICelera
Cytogenetic Map16q22.3NCBI
HuRef1658,894,249 - 58,895,674 (+)NCBIHuRef
CHM1_11674,539,058 - 74,540,483 (+)NCBICHM1_1
T2T-CHM13v2.01678,910,078 - 78,911,503 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932   PMID:20130911   PMID:23314567  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 16q22.1-24.1(chr16:70414573-84908120)x1 copy number loss See cases [RCV000133814] Chr16:70414573..84908120 [GRCh38]
Chr16:70448476..84941726 [GRCh37]
Chr16:69005977..83499227 [NCBI36]
Chr16:16q22.1-24.1
pathogenic
GRCh38/hg38 16q22.3(chr16:72853152-73376761)x3 copy number gain See cases [RCV000134457] Chr16:72853152..73376761 [GRCh38]
Chr16:72887051..73410660 [GRCh37]
Chr16:71444552..71968161 [NCBI36]
Chr16:16q22.3
benign
GRCh38/hg38 16q21-24.1(chr16:62925929-84585795)x3 copy number gain See cases [RCV000135863] Chr16:62925929..84585795 [GRCh38]
Chr16:62959833..84619401 [GRCh37]
Chr16:61517334..83176902 [NCBI36]
Chr16:16q21-24.1
pathogenic
GRCh38/hg38 16q22.1-24.3(chr16:70749398-90096995)x3 copy number gain See cases [RCV000137495] Chr16:70749398..90096995 [GRCh38]
Chr16:70783301..90163403 [GRCh37]
Chr16:69340802..88690904 [NCBI36]
Chr16:16q22.1-24.3
pathogenic
GRCh38/hg38 16q21-24.3(chr16:65511483-90096995)x3 copy number gain See cases [RCV000139426] Chr16:65511483..90096995 [GRCh38]
Chr16:65545386..90163403 [GRCh37]
Chr16:64102887..88690904 [NCBI36]
Chr16:16q21-24.3
pathogenic
GRCh38/hg38 16q22.1-23.3(chr16:69053457-83274681)x3 copy number gain See cases [RCV000142038] Chr16:69053457..83274681 [GRCh38]
Chr16:69087360..83308286 [GRCh37]
Chr16:67644861..81865787 [NCBI36]
Chr16:16q22.1-23.3
pathogenic
GRCh38/hg38 16q21-24.3(chr16:64389378-90081985)x3 copy number gain See cases [RCV000142578] Chr16:64389378..90081985 [GRCh38]
Chr16:64423281..90148393 [GRCh37]
Chr16:62980782..88675894 [NCBI36]
Chr16:16q21-24.3
pathogenic|likely pathogenic
GRCh38/hg38 16q12.2-24.3(chr16:52899183-90088654)x3 copy number gain See cases [RCV000143425] Chr16:52899183..90088654 [GRCh38]
Chr16:52933095..90155062 [GRCh37]
Chr16:51490596..88682563 [NCBI36]
Chr16:16q12.2-24.3
pathogenic
GRCh38/hg38 16q21-23.3(chr16:65957829-83611443)x3 copy number gain See cases [RCV000143742] Chr16:65957829..83611443 [GRCh38]
Chr16:65991732..83645048 [GRCh37]
Chr16:64549233..82202549 [NCBI36]
Chr16:16q21-23.3
pathogenic
GRCh38/hg38 16q22.3-23.1(chr16:73012737-74289420)x1 copy number loss See cases [RCV000052001] Chr16:73012737..74289420 [GRCh38]
Chr16:73046636..74323318 [GRCh37]
Chr16:71604137..72880819 [NCBI36]
Chr16:16q22.3-23.1
uncertain significance
GRCh38/hg38 16q21-23.1(chr16:58456122-74708723)x3 copy number gain See cases [RCV000052408] Chr16:58456122..74708723 [GRCh38]
Chr16:58490026..74742621 [GRCh37]
Chr16:57047527..73300122 [NCBI36]
Chr16:16q21-23.1
pathogenic
GRCh38/hg38 16q21-24.3(chr16:65313395-90081985)x3 copy number gain See cases [RCV000052421] Chr16:65313395..90081985 [GRCh38]
Chr16:65347298..90148393 [GRCh37]
Chr16:63904799..88675894 [NCBI36]
Chr16:16q21-24.3
pathogenic
GRCh38/hg38 16q22.1-24.3(chr16:70514631-90081985)x3 copy number gain See cases [RCV000052422] Chr16:70514631..90081985 [GRCh38]
Chr16:70548534..90148393 [GRCh37]
Chr16:69106035..88675894 [NCBI36]
Chr16:16q22.1-24.3
pathogenic
GRCh38/hg38 16q22.1-23.1(chr16:68698941-74353205)x1 copy number loss See cases [RCV000053337] Chr16:68698941..74353205 [GRCh38]
Chr16:68732844..74387103 [GRCh37]
Chr16:67290345..72944604 [NCBI36]
Chr16:16q22.1-23.1
pathogenic
GRCh38/hg38 16q22.1-23.1(chr16:69918076-76723348)x1 copy number loss See cases [RCV000053356] Chr16:69918076..76723348 [GRCh38]
Chr16:69951979..76757245 [GRCh37]
Chr16:68509480..75314746 [NCBI36]
Chr16:16q22.1-23.1
pathogenic
GRCh38/hg38 16q22.3-23.3(chr16:73049467-82576326)x1 copy number loss See cases [RCV000053357] Chr16:73049467..82576326 [GRCh38]
Chr16:73083366..82609931 [GRCh37]
Chr16:71640867..81167432 [NCBI36]
Chr16:16q22.3-23.3
pathogenic
GRCh38/hg38 16q22.2-22.3(chr16:71279916-73246687)x3 copy number gain See cases [RCV000053867] Chr16:71279916..73246687 [GRCh38]
Chr16:71313819..73280586 [GRCh37]
Chr16:69871320..71838087 [NCBI36]
Chr16:16q22.2-22.3
uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:121
Count of miRNA genes:116
Interacting mature miRNAs:121
Transcripts:ENST00000569990
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
High
Medium 3 21 1 2
Low 40 1200 35 3 1 799 72 206 10 42 88 46 714
Below cutoff 1179 523 681 122 207 82 1852 1287 2090 231 712 810 42 653 1296

Sequence


RefSeq Acc Id: ENST00000569990
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1673,092,349 - 73,093,774 (+)Ensembl
RefSeq Acc Id: ENST00000642127
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1673,092,690 - 73,099,337 (+)Ensembl
RefSeq Acc Id: ENST00000647808
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1673,092,690 - 73,094,546 (+)Ensembl
RefSeq Acc Id: ENST00000659438
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1673,092,508 - 73,093,772 (+)Ensembl
RefSeq Acc Id: ENST00000662824
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1673,092,508 - 73,093,766 (+)Ensembl
RefSeq Acc Id: NR_027756
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381673,092,349 - 73,093,774 (+)NCBI
GRCh371673,126,248 - 73,127,673 (+)NCBI
HuRef1658,894,249 - 58,895,674 (+)NCBI
CHM1_11674,539,058 - 74,540,483 (+)NCBI
T2T-CHM13v2.01678,910,078 - 78,911,503 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein ACI46634 (Get FASTA)   NCBI Sequence Viewer  
  ACI46635 (Get FASTA)   NCBI Sequence Viewer  
  EAW59167 (Get FASTA)   NCBI Sequence Viewer  


Additional Information

Database Acc Id Source(s)
COSMIC HCCAT5 COSMIC
Ensembl Genes ENSG00000260880 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000569990 ENTREZGENE
GTEx ENSG00000260880 GTEx
HGNC ID HGNC:48612 ENTREZGENE
Human Proteome Map HCCAT5 Human Proteome Map
NCBI Gene HCCAT5 ENTREZGENE
OMIM 615613 OMIM
RNAcentral URS000075E6F4 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 HCCAT5  hepatocellular carcinoma associated transcript 5    hepatocellular carcinoma associated transcript 5 (non-protein coding)  Symbol and/or name change 5135510 APPROVED