ZNF594-DT (ZNF594 divergent transcript) - Rat Genome Database

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Gene: ZNF594-DT (ZNF594 divergent transcript) Homo sapiens
Analyze
Symbol: ZNF594-DT
Name: ZNF594 divergent transcript
RGD ID: 16563479
HGNC Page HGNC:55347
Description: ASSOCIATED WITH genetic disease; head and neck cancer; Neoplasm of head and neck; INTERACTS WITH 17beta-estradiol; acrylamide
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC087500.1; LOC100130950; novel transcript, antisense to C17orf87; uncharacterized LOC100130950
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38175,192,007 - 5,236,003 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl175,192,007 - 5,248,182 (+)EnsemblGRCh38hg38GRCh38
GRCh37175,095,302 - 5,139,298 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map17p13.2NCBI
HuRef174,985,611 - 5,029,047 (+)NCBIHuRef
CHM1_1175,105,048 - 5,148,686 (+)NCBICHM1_1
T2T-CHM13v2.0175,085,356 - 5,129,409 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:24162737  


Genomics

Variants

.
Variants in ZNF594-DT
5 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17p13.2-13.1(chr17:3601515-7178024)x1 copy number loss See cases [RCV000053406] Chr17:3601515..7178024 [GRCh38]
Chr17:3504809..7081343 [GRCh37]
Chr17:3451558..7022067 [NCBI36]
Chr17:17p13.2-13.1		 pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:162016-7697012)x1 copy number loss See cases [RCV000138214] Chr17:162016..7697012 [GRCh38]
Chr17:45835..7600330 [GRCh37]
Chr17:11807..7541055 [NCBI36]
Chr17:17p13.3-13.1		 pathogenic
GRCh38/hg38 17p13.3-12(chr17:150732-14764202)x3 copy number gain See cases [RCV000142236] Chr17:150732..14764202 [GRCh38]
Chr17:525..14667519 [GRCh37]
Chr17:525..14608244 [NCBI36]
Chr17:17p13.3-12		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:2062380-5258340)x1 copy number loss See cases [RCV000133721] Chr17:2062380..5258340 [GRCh38]
Chr17:1965674..5161635 [GRCh37]
Chr17:1912424..5102359 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:162088-6959050)x1 copy number loss See cases [RCV000134135] Chr17:162088..6959050 [GRCh38]
Chr17:45835..6862369 [GRCh37]
Chr17:11879..6803093 [NCBI36]
Chr17:17p13.3-13.1		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:150732-5935377)x1 copy number loss See cases [RCV000141658] Chr17:150732..5935377 [GRCh38]
Chr17:525..5838697 [GRCh37]
Chr17:525..5779421 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.2(chr17:4092608-5354473)x3 copy number gain See cases [RCV000139650] Chr17:4092608..5354473 [GRCh38]
Chr17:3995902..5257768 [GRCh37]
Chr17:3942651..5198492 [NCBI36]
Chr17:17p13.2		 likely benign
GRCh38/hg38 17p13.3-13.2(chr17:193307-5652222)x1 copy number loss See cases [RCV000053384] Chr17:193307..5652222 [GRCh38]
Chr17:45835..5555542 [GRCh37]
Chr17:43098..5496266 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
NM_207103.3(SCIMP):c.99T>C (p.Gly33=) single nucleotide variant Head and neck cancer [RCV001004027] Chr17:5223379 [GRCh38]
Chr17:5126674 [GRCh37]
Chr17:17p13.2		 uncertain significance
GRCh38/hg38 17p13.2(chr17:4044302-5943772)x1 copy number loss See cases [RCV000135548] Chr17:4044302..5943772 [GRCh38]
Chr17:3947596..5847092 [GRCh37]
Chr17:3894345..5787816 [NCBI36]
Chr17:17p13.2		 likely pathogenic
GRCh38/hg38 17p13.3-12(chr17:162016-12343901)x3 copy number gain See cases [RCV000138531] Chr17:162016..12343901 [GRCh38]
Chr17:45835..12247218 [GRCh37]
Chr17:11807..12187943 [NCBI36]
Chr17:17p13.3-12		 pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:198748-7491129)x3 copy number gain See cases [RCV000134970] Chr17:198748..7491129 [GRCh38]
Chr17:50690..7394448 [GRCh37]
Chr17:48539..7335172 [NCBI36]
Chr17:17p13.3-13.1		 pathogenic
GRCh38/hg38 17p13.2(chr17:4915519-5197126)x1 copy number loss See cases [RCV000141706] Chr17:4915519..5197126 [GRCh38]
Chr17:4818814..5100421 [GRCh37]
Chr17:4759591..5041145 [NCBI36]
Chr17:17p13.2		 likely pathogenic|uncertain significance
NM_207103.3(SCIMP):c.271C>G (p.Leu91Val) single nucleotide variant Inborn genetic diseases [RCV002678026] Chr17:5214937 [GRCh38]
Chr17:5118232 [GRCh37]
Chr17:17p13.2		 uncertain significance
NM_207103.3(SCIMP):c.12C>A (p.Phe4Leu) single nucleotide variant Inborn genetic diseases [RCV002656725] Chr17:5234744 [GRCh38]
Chr17:5138039 [GRCh37]
Chr17:17p13.2		 likely benign
GRCh38/hg38 17p13.3-12(chr17:165730-11404096)x3 copy number gain Chromosome 17p13.3 duplication syndrome [RCV003327726] Chr17:165730..11404096 [GRCh38]
Chr17:17p13.3-12		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:719
Count of miRNA genes:533
Interacting mature miRNAs:581
Transcripts:ENST00000571689, ENST00000573772, ENST00000575601
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 adipose tissue appendage entire extraembryonic component
High
Medium 38 48 7 27 7 36 33
Low 2372 2313 1514 465 1404 310 4058 1763 3465 390 1394 1549 167 1107 2544 3
Below cutoff 56 664 169 155 488 152 295 422 216 19 16 23 3 97 243 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000571689
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,192,104 - 5,235,643 (+)Ensembl
RefSeq Acc Id: ENST00000573772
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,192,007 - 5,248,182 (+)Ensembl
RefSeq Acc Id: ENST00000575601
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,192,084 - 5,223,643 (+)Ensembl
RefSeq Acc Id: ENST00000649359
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,192,090 - 5,235,637 (+)Ensembl
RefSeq Acc Id: ENST00000656594
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,215,187 - 5,223,998 (+)Ensembl
RefSeq Acc Id: ENST00000663434
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,192,068 - 5,235,605 (+)Ensembl
RefSeq Acc Id: ENST00000667038
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,192,090 - 5,231,761 (+)Ensembl
RefSeq Acc Id: ENST00000669386
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,192,027 - 5,235,995 (+)Ensembl
RefSeq Acc Id: ENST00000671211
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,192,042 - 5,240,109 (+)Ensembl
RefSeq Acc Id: ENST00000702138
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl175,234,947 - 5,235,622 (+)Ensembl
RefSeq Acc Id: NR_034082
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38175,192,007 - 5,236,003 (+)NCBI
T2T-CHM13v2.0175,085,356 - 5,129,409 (+)NCBI
Sequence:
RefSeq Acc Id: NR_152840
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38175,192,007 - 5,236,003 (+)NCBI
T2T-CHM13v2.0175,085,356 - 5,129,409 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein EAW90346 (Get FASTA)   NCBI Sequence Viewer  
  EAW90347 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC ZNF594-DT COSMIC
Ensembl Genes ENSG00000261879 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000669386 ENTREZGENE
GTEx ENSG00000261879 GTEx
HGNC ID HGNC:55347 ENTREZGENE
Human Proteome Map ZNF594-DT Human Proteome Map
NCBI Gene LOC100130950 ENTREZGENE
RNAcentral URS0000CCE035 RNACentral
  URS0000CCE08B RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-11-09 ZNF594-DT  ZNF594 divergent transcript  AC087500.1  novel transcript, antisense to C17orf87  Symbol and/or name change 19259463 PROVISIONAL
2020-06-25 AC087500.1  novel transcript, antisense to C17orf87  LOC100130950  uncharacterized LOC100130950  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC100130950  uncharacterized LOC100130950  AC087500.1  novel transcript, antisense to C17orf87  Symbol and/or name change 5135510 APPROVED