CTC-338M12.4 (uncharacterized LOC101928649) - Rat Genome Database

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Gene: CTC-338M12.4 (uncharacterized LOC101928649) Homo sapiens
Analyze
Symbol: CTC-338M12.4
Name: uncharacterized LOC101928649
RGD ID: 16555777
Description: INTERACTS WITH aristolochic acid A; crocidolite asbestos; propofol
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC008443.1; novel transcript, antisense to TRIM52
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385181,246,541 - 181,257,586 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5181,246,466 - 181,295,573 (+)EnsemblGRCh38hg38GRCh38
GRCh375180,673,541 - 180,684,587 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q35.3NCBI
HuRef5175,400,450 - 175,411,694 (+)NCBIHuRef
CHM1_15180,105,912 - 180,117,155 (+)NCBICHM1_1
T2T-CHM13v2.05181,806,493 - 181,817,539 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:8889548  


Genomics

Variants

.
Variants in CTC-338M12.4
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q32-35.3(chr5:149714592-181272151)x3 copy number gain See cases [RCV000051863] Chr5:149714592..181272151 [GRCh38]
Chr5:149094155..180699152 [GRCh37]
Chr5:149074348..180631758 [NCBI36]
Chr5:5q32-35.3		 pathogenic
GRCh38/hg38 5q35.3(chr5:178235909-181292788)x3 copy number gain See cases [RCV000142298] Chr5:178235909..181292788 [GRCh38]
Chr5:177662910..180719789 [GRCh37]
Chr5:177595516..180652395 [NCBI36]
Chr5:5q35.3		 likely pathogenic
GRCh38/hg38 5q35.3(chr5:180636182-181269805)x3 copy number gain See cases [RCV000136903] Chr5:180636182..181269805 [GRCh38]
Chr5:180063182..180696806 [GRCh37]
Chr5:179995788..180629412 [NCBI36]
Chr5:5q35.3		 uncertain significance
GRCh38/hg38 5q35.2-35.3(chr5:176700128-181269805)x1 copy number loss See cases [RCV000142648] Chr5:176700128..181269805 [GRCh38]
Chr5:176127129..180696806 [GRCh37]
Chr5:176059735..180629412 [NCBI36]
Chr5:5q35.2-35.3		 pathogenic
GRCh38/hg38 5q35.2-35.3(chr5:175536771-181292788)x1 copy number loss See cases [RCV000141987] Chr5:175536771..181292788 [GRCh38]
Chr5:174963774..180719789 [GRCh37]
Chr5:174896380..180652395 [NCBI36]
Chr5:5q35.2-35.3		 pathogenic
GRCh38/hg38 5q35.3(chr5:178529878-181269805)x3 copy number gain See cases [RCV000051205] Chr5:178529878..181269805 [GRCh38]
Chr5:177956879..180696806 [GRCh37]
Chr5:177889485..180629412 [NCBI36]
Chr5:5q35.3		 uncertain significance
GRCh38/hg38 5q34-35.3(chr5:168689326-181269946)x3 copy number gain See cases [RCV000051866] Chr5:168689326..181269946 [GRCh38]
Chr5:168116331..180696947 [GRCh37]
Chr5:168048909..180629553 [NCBI36]
Chr5:5q34-35.3		 pathogenic
GRCh38/hg38 5q33.3-35.3(chr5:156825512-181269805)x3 copy number gain See cases [RCV000133847] Chr5:156825512..181269805 [GRCh38]
Chr5:156252523..180696806 [GRCh37]
Chr5:156185101..180629412 [NCBI36]
Chr5:5q33.3-35.3		 pathogenic
GRCh38/hg38 5q34-35.3(chr5:164386701-181269805)x3 copy number gain See cases [RCV000135546] Chr5:164386701..181269805 [GRCh38]
Chr5:163813707..180696806 [GRCh37]
Chr5:163746285..180629412 [NCBI36]
Chr5:5q34-35.3		 pathogenic
GRCh38/hg38 5q35.3(chr5:181249063-181285203)x1 copy number loss See cases [RCV000135182] Chr5:181249063..181285203 [GRCh38]
Chr5:180676063..180712204 [GRCh37]
Chr5:180608669..180644810 [NCBI36]
Chr5:5q35.3		 likely benign
GRCh38/hg38 5q35.1-35.3(chr5:169334755-181285301)x3 copy number gain See cases [RCV000141249] Chr5:169334755..181285301 [GRCh38]
Chr5:168761759..180712302 [GRCh37]
Chr5:168694337..180644908 [NCBI36]
Chr5:5q35.1-35.3		 pathogenic
NM_001346048.2(TRIM52):c.814-613T>C single nucleotide variant not specified [RCV004336679] Chr5:181257472 [GRCh38]
Chr5:180684473 [GRCh37]
Chr5:5q35.3		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:867
Count of miRNA genes:563
Interacting mature miRNAs:619
Transcripts:ENST00000417281, ENST00000505151, ENST00000506340, ENST00000511331, ENST00000599439
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 sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 41 41 50 4 55 7 63 32 66 16 94 97 1 39 2
Low 2395 2636 1572 521 1712 359 4293 2028 3440 397 1360 1513 174 1 1203 2749 4 2
Below cutoff 3 312 103 98 181 98 1 136 228 5 6 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000417281
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5181,247,701 - 181,257,586 (+)Ensembl
RefSeq Acc Id: ENST00000505151
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5181,246,466 - 181,257,586 (+)Ensembl
RefSeq Acc Id: ENST00000506340
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5181,246,493 - 181,257,586 (+)Ensembl
RefSeq Acc Id: ENST00000511331
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5181,246,523 - 181,272,167 (+)Ensembl
RefSeq Acc Id: ENST00000599439
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5181,255,719 - 181,257,586 (+)Ensembl
RefSeq Acc Id: NR_109909
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385181,246,541 - 181,257,586 (+)NCBI
T2T-CHM13v2.05181,806,493 - 181,817,539 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC CTC-338M12.4 COSMIC
Ensembl Genes ENSG00000233937 Ensembl
  ENSG00000248275 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000715343 ENTREZGENE
GTEx ENSG00000233937 GTEx
  ENSG00000248275 GTEx
Human Proteome Map CTC-338M12.4 Human Proteome Map
NCBI Gene CTC-338M12.4 ENTREZGENE
RNAcentral URS000075CE02 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-08-20 CTC-338M12.4  uncharacterized LOC101928649  AC008443.1  novel transcript, antisense to TRIM52  Symbol and/or name change 19259462 PROVISIONAL
2020-06-25 AC008443.1  novel transcript, antisense to TRIM52  CTC-338M12.4  uncharacterized LOC101928649  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 CTC-338M12.4  uncharacterized LOC101928649  AC008443.1  novel transcript, antisense to TRIM52  Symbol and/or name change 5135510 APPROVED