ARHGEF38-IT1 (ARHGEF38 intronic transcript 1) - Rat Genome Database

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Gene: ARHGEF38-IT1 (ARHGEF38 intronic transcript 1) Homo sapiens
Analyze
Symbol: ARHGEF38-IT1
Name: ARHGEF38 intronic transcript 1
RGD ID: 6480965
HGNC Page HGNC:41483
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: PREDICTED
Previously known as: AC004066.5
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384105,561,591 - 105,570,238 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4105,561,591 - 105,570,238 (+)EnsemblGRCh38hg38GRCh38
GRCh374106,482,748 - 106,491,395 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map4q24NCBI
HuRef4102,217,283 - 102,225,930 (+)NCBIHuRef
CHM1_14106,459,558 - 106,468,204 (+)NCBICHM1_1
T2T-CHM13v2.04108,872,392 - 108,881,039 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q22.2-32.3(chr4:92913386-165299707)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|See cases [RCV000051775] Chr4:92913386..165299707 [GRCh38]
Chr4:93834537..166220859 [GRCh37]
Chr4:94053560..166440309 [NCBI36]
Chr4:4q22.2-32.3		 pathogenic
GRCh38/hg38 4q22.3-28.3(chr4:96092893-136410207)x3 copy number gain See cases [RCV000051776] Chr4:96092893..136410207 [GRCh38]
Chr4:97014044..137331362 [GRCh37]
Chr4:97233067..137550812 [NCBI36]
Chr4:4q22.3-28.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:38
Interacting mature miRNAs:38
Transcripts:ENST00000512262
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 1 31 1
Low 228 2 353 152 49 22 178 2 145 82 482 477 132 5 102
Below cutoff 537 48 485 93 118 77 586 36 172 143 225 566 17 26 345 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000512262
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4105,561,591 - 105,570,238 (+)Ensembl
RefSeq Acc Id: NR_046840
RefSeq Status: PREDICTED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384105,561,591 - 105,570,238 (+)NCBI
GRCh374106,482,748 - 106,491,395 (+)NCBI
HuRef4102,217,283 - 102,225,930 (+)NCBI
CHM1_14106,459,558 - 106,468,204 (+)NCBI
T2T-CHM13v2.04108,872,392 - 108,881,039 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC ARHGEF38-IT1 COSMIC
Ensembl Genes ENSG00000249885 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000512262 ENTREZGENE
GTEx ENSG00000249885 GTEx
HGNC ID HGNC:41483 ENTREZGENE
Human Proteome Map ARHGEF38-IT1 Human Proteome Map
NCBI Gene ARHGEF38-IT1 ENTREZGENE
RNAcentral URS00001EFACC RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-03-03 ARHGEF38-IT1  ARHGEF38 intronic transcript 1    ARHGEF38 intronic transcript 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED