WDR5B-DT (WDR5B divergent transcript) - Rat Genome Database

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Gene: WDR5B-DT (WDR5B divergent transcript) Homo sapiens
Analyze
Symbol: WDR5B-DT
Name: WDR5B divergent transcript
RGD ID: 16566534
HGNC Page HGNC:55192
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC083798.2; LOC102723582; novel transcript, antisense to KPNA1; uncharacterized LOC102723582
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383122,416,206 - 122,443,247 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3122,416,200 - 122,443,180 (+)EnsemblGRCh38hg38GRCh38
GRCh373122,135,053 - 122,162,094 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3q21.1NCBI
CHM1_13122,098,538 - 122,125,579 (+)NCBICHM1_1
T2T-CHM13v2.03125,135,761 - 125,162,471 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:16344560  


Genomics

Variants

.
Variants in WDR5B-DT
10 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q13.33-21.3(chr3:121925147-126782249)x1 copy number loss See cases [RCV000140814] Chr3:121925147..126782249 [GRCh38]
Chr3:121643994..126501092 [GRCh37]
Chr3:123126684..127983782 [NCBI36]
Chr3:3q13.33-21.3		 pathogenic
GRCh38/hg38 3q13.31-21.2(chr3:114122562-124532374)x1 copy number loss See cases [RCV000142009] Chr3:114122562..124532374 [GRCh38]
Chr3:113841409..124251221 [GRCh37]
Chr3:115324099..125733911 [NCBI36]
Chr3:3q13.31-21.2		 pathogenic
GRCh38/hg38 3q13.32-21.2(chr3:119117166-125920734)x1 copy number loss See cases [RCV000051546] Chr3:119117166..125920734 [GRCh38]
Chr3:118836013..125639577 [GRCh37]
Chr3:120318703..127122267 [NCBI36]
Chr3:3q13.32-21.2		 pathogenic
GRCh38/hg38 3q13.33-21.2(chr3:121644209-125676353)x1 copy number loss See cases [RCV000051569] Chr3:121644209..125676353 [GRCh38]
Chr3:121363056..125395197 [GRCh37]
Chr3:122845746..126877887 [NCBI36]
Chr3:3q13.33-21.2		 pathogenic
NM_002264.4(KPNA1):c.1185G>A (p.Arg395=) single nucleotide variant not provided [RCV000954898] Chr3:122433726 [GRCh38]
Chr3:122152573 [GRCh37]
Chr3:3q21.1		 benign
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24		 pathogenic
GRCh38/hg38 3q13.32-21.3(chr3:118673898-126540730)x1 copy number loss See cases [RCV000143695] Chr3:118673898..126540730 [GRCh38]
Chr3:118392745..126259573 [GRCh37]
Chr3:119875435..127742263 [NCBI36]
Chr3:3q13.32-21.3		 pathogenic
GRCh38/hg38 3q13.2-21.3(chr3:112620977-128734134)x1 copy number loss See cases [RCV000139033] Chr3:112620977..128734134 [GRCh38]
Chr3:112339824..128452977 [GRCh37]
Chr3:113822514..129935667 [NCBI36]
Chr3:3q13.2-21.3		 pathogenic
GRCh38/hg38 3q13.31-21.1(chr3:115019074-122513398)x1 copy number loss See cases [RCV000135961] Chr3:115019074..122513398 [GRCh38]
Chr3:114737921..122232245 [GRCh37]
Chr3:116220611..123714935 [NCBI36]
Chr3:3q13.31-21.1		 pathogenic
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1 copy number loss See cases [RCV000051543] Chr3:93886671..123216683 [GRCh38]
Chr3:93605515..122935530 [GRCh37]
Chr3:95088205..124418220 [NCBI36]
Chr3:3q11.1-21.1		 pathogenic
Single allele duplication not specified [RCV002286365] Chr3:122157406..123113479 [GRCh38]
Chr3:3q13.33-21.1		 uncertain significance
NM_002264.4(KPNA1):c.1537A>G (p.Ile513Val) single nucleotide variant not specified [RCV004242650] Chr3:122427065 [GRCh38]
Chr3:122145912 [GRCh37]
Chr3:3q21.1		 uncertain significance
NM_002264.4(KPNA1):c.1258G>A (p.Val420Ile) single nucleotide variant not specified [RCV004120468] Chr3:122427709 [GRCh38]
Chr3:122146556 [GRCh37]
Chr3:3q21.1		 uncertain significance
NM_002264.4(KPNA1):c.1426T>G (p.Tyr476Asp) single nucleotide variant not specified [RCV004177881] Chr3:122427541 [GRCh38]
Chr3:122146388 [GRCh37]
Chr3:3q21.1		 uncertain significance
GRCh38/hg38 3q11.1-21.2(chr3:93979547-124774010)x1 copy number loss Chromosome 3q13.31 deletion syndrome [RCV003327614] Chr3:93979547..124774010 [GRCh38]
Chr3:3q11.1-21.2		 pathogenic
NM_002264.4(KPNA1):c.1022A>G (p.Gln341Arg) single nucleotide variant not specified [RCV004412030] Chr3:122437270 [GRCh38]
Chr3:122156117 [GRCh37]
Chr3:3q21.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:737
Count of miRNA genes:566
Interacting mature miRNAs:625
Transcripts:ENST00000608015, ENST00000608346, ENST00000608465, ENST00000608756, ENST00000609469
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 1 1 19 1 3 23 4
Low 2383 2322 1529 428 1643 272 4273 1840 3173 378 1412 1590 168 1199 2726 4
Below cutoff 48 659 193 194 284 192 82 352 531 40 13 14 2 5 62

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000608015
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3122,416,225 - 122,426,344 (+)Ensembl
RefSeq Acc Id: ENST00000608346
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3122,416,219 - 122,433,262 (+)Ensembl
RefSeq Acc Id: ENST00000608465
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3122,416,225 - 122,421,404 (+)Ensembl
RefSeq Acc Id: ENST00000608756
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3122,416,207 - 122,427,240 (+)Ensembl
RefSeq Acc Id: ENST00000609469
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3122,416,207 - 122,443,180 (+)Ensembl
RefSeq Acc Id: ENST00000667395
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3122,416,205 - 122,421,402 (+)Ensembl
RefSeq Acc Id: ENST00000686885
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3122,416,200 - 122,421,404 (+)Ensembl
RefSeq Acc Id: NR_125405
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383122,416,206 - 122,443,247 (+)NCBI
T2T-CHM13v2.03125,135,761 - 125,162,471 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC WDR5B-DT COSMIC
Ensembl Genes ENSG00000272758 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000609469 ENTREZGENE
GTEx ENSG00000272758 GTEx
HGNC ID HGNC:55192 ENTREZGENE
Human Proteome Map WDR5B-DT Human Proteome Map
NCBI Gene LOC102723582 ENTREZGENE
RNAcentral URS00007E3FA0 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-08-17 WDR5B-DT  WDR5B divergent transcript  AC083798.2  novel transcript, antisense to KPNA1  Symbol and/or name change 19259463 PROVISIONAL
2020-06-25 AC083798.2  novel transcript, antisense to KPNA1  LOC102723582  uncharacterized LOC102723582  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC102723582  uncharacterized LOC102723582  AC083798.2  novel transcript, antisense to KPNA1  Symbol and/or name change 5135510 APPROVED