RNPC3-DT (RNPC3 divergent transcript) - Rat Genome Database

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Gene: RNPC3-DT (RNPC3 divergent transcript) Homo sapiens
Analyze
Symbol: RNPC3-DT
Name: RNPC3 divergent transcript
RGD ID: 16552944
HGNC Page HGNC:55855
Description: ASSOCIATED WITH Autism; autistic disorder
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC095032.1; LOC101928436; uncharacterized LOC101928436
RGD Orthologs
Green Monkey
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381103,416,980 - 103,525,508 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1103,415,980 - 103,525,511 (-)EnsemblGRCh38hg38GRCh38
GRCh371103,959,602 - 104,068,130 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1p21.1NCBI
HuRef1102,016,793 - 102,030,949 (-)NCBIHuRef
T2T-CHM13v2.01103,265,909 - 103,374,433 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Autism  (IAGP)
References
Additional References at PubMed
PMID:23251661  


Genomics

Comparative Map Data
RNPC3-DT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381103,416,980 - 103,525,508 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1103,415,980 - 103,525,511 (-)EnsemblGRCh38hg38GRCh38
GRCh371103,959,602 - 104,068,130 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1p21.1NCBI
HuRef1102,016,793 - 102,030,949 (-)NCBIHuRef
T2T-CHM13v2.01103,265,909 - 103,374,433 (-)NCBIT2T-CHM13v2.0
LOC103225894
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12029,893,811 - 29,998,718 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603828,151,292 - 28,262,172 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in RNPC3-DT
7 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p21.3-13.3(chr1:97410602-110670510)x1 copy number loss See cases [RCV000053877] Chr1:97410602..110670510 [GRCh38]
Chr1:97876158..111213132 [GRCh37]
Chr1:97648746..111014655 [NCBI36]
Chr1:1p21.3-13.3		 pathogenic
GRCh38/hg38 1p21.2-13.2(chr1:101618097-111703028)x1 copy number loss See cases [RCV000053879] Chr1:101618097..111703028 [GRCh38]
Chr1:102083653..112245650 [GRCh37]
Chr1:101856241..112047173 [NCBI36]
Chr1:1p21.2-13.2		 pathogenic
GRCh38/hg38 1p21.1(chr1:103108301-103564967)x3 copy number gain See cases [RCV000134889] Chr1:103108301..103564967 [GRCh38]
Chr1:103573857..104107589 [GRCh37]
Chr1:103346445..103909112 [NCBI36]
Chr1:1p21.1		 uncertain significance
GRCh38/hg38 1p21.1(chr1:103082841-103618409)x3 copy number gain See cases [RCV000140408] Chr1:103082841..103618409 [GRCh38]
Chr1:103548397..104161031 [GRCh37]
Chr1:103320985..103962554 [NCBI36]
Chr1:1p21.1		 uncertain significance
GRCh38/hg38 1p21.1-13.3(chr1:103474348-106724941)x1 copy number loss See cases [RCV000139512] Chr1:103474348..106724941 [GRCh38]
Chr1:104016970..107267563 [GRCh37]
Chr1:103789558..107069086 [NCBI36]
Chr1:1p21.1-13.3		 uncertain significance
GRCh38/hg38 1p21.1(chr1:103280931-103754679)x1 copy number loss See cases [RCV000135887] Chr1:103280931..103754679 [GRCh38]
Chr1:103746487..104297301 [GRCh37]
Chr1:103519075..104098824 [NCBI36]
Chr1:1p21.1		 benign
GRCh38/hg38 1p21.1(chr1:102983807-105059200)x1 copy number loss See cases [RCV000141371] Chr1:102983807..105059200 [GRCh38]
Chr1:103449363..105601822 [GRCh37]
Chr1:103221951..105403345 [NCBI36]
Chr1:1p21.1		 uncertain significance
GRCh38/hg38 1p31.1-21.1(chr1:83457325-104273917)x3 copy number gain See cases [RCV000135654] Chr1:83457325..104273917 [GRCh38]
Chr1:83923008..104816539 [GRCh37]
Chr1:83695596..104618062 [NCBI36]
Chr1:1p31.1-21.1		 pathogenic
GRCh38/hg38 1p21.1(chr1:103462283-103612668)x3 copy number gain See cases [RCV000143009] Chr1:103462283..103612668 [GRCh38]
Chr1:104004905..104155290 [GRCh37]
Chr1:103777493..103956813 [NCBI36]
Chr1:1p21.1		 likely benign
NC_000001.11:g.(?_103175204)_(111410059_?)del deletion Autism [RCV000754122] Chr1:103175204..111410059 [GRCh38]
Chr1:1p21.1-13.2		 likely pathogenic
GRCh38/hg38 1p21.3-13.3(chr1:97272349-108893138)x1 copy number loss See cases [RCV000135333] Chr1:97272349..108893138 [GRCh38]
Chr1:97737905..109435760 [GRCh37]
Chr1:97510493..109237283 [NCBI36]
Chr1:1p21.3-13.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:121
Count of miRNA genes:116
Interacting mature miRNAs:117
Transcripts:ENST00000444810, ENST00000447322
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
Low 64 108 108 4 43 1 229 60 574 19 444 90 3 139 141 2
Below cutoff 1153 1012 717 150 319 80 1802 971 2120 149 494 813 79 747 1216 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000444810
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1103,417,023 - 103,525,511 (-)Ensembl
RefSeq Acc Id: ENST00000447322
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1103,416,700 - 103,525,508 (-)Ensembl
RefSeq Acc Id: ENST00000662345
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1103,415,980 - 103,525,504 (-)Ensembl
RefSeq Acc Id: ENST00000668150
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1103,416,623 - 103,525,508 (-)Ensembl
RefSeq Acc Id: NR_168319
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381103,416,980 - 103,525,508 (-)NCBI
T2T-CHM13v2.01103,265,909 - 103,374,433 (-)NCBI
Sequence:
RefSeq Acc Id: NR_168320
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381103,416,980 - 103,525,508 (-)NCBI
T2T-CHM13v2.01103,265,909 - 103,374,433 (-)NCBI
Sequence:
RefSeq Acc Id: NR_168321
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381103,416,980 - 103,525,508 (-)NCBI
T2T-CHM13v2.01103,265,909 - 103,374,433 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC RNPC3-DT COSMIC
Ensembl Genes ENSG00000224613 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000444810 ENTREZGENE
  ENST00000668150 ENTREZGENE
GTEx ENSG00000224613 GTEx
HGNC ID HGNC:55855 ENTREZGENE
Human Proteome Map RNPC3-DT Human Proteome Map
NCBI Gene LOC101928436 ENTREZGENE
RNAcentral URS0001BBE511 RNACentral
  URS0001BBE534 RNACentral
  URS0001BBE5D0 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-09-06 RNPC3-DT  RNPC3 divergent transcript  AC095032.1  novel transcript  Symbol and/or name change 19259463 PROVISIONAL
2020-12-03 AC095032.1  novel transcript  AC095032.1  uncharacterized LOC101928436  Symbol and/or name change 19259462 PROVISIONAL
2020-06-25 AC095032.1  uncharacterized LOC101928436  LOC101928436  uncharacterized LOC101928436  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC101928436  uncharacterized LOC101928436  AC095032.1  uncharacterized LOC101928436  Symbol and/or name change 5135510 APPROVED