SMC5-DT (SMC5 divergent transcript) - Rat Genome Database

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Gene: SMC5-DT (SMC5 divergent transcript) Homo sapiens
Analyze
Symbol: SMC5-DT
Name: SMC5 divergent transcript
RGD ID: 7246425
HGNC Page HGNC:48718
Description: ASSOCIATED WITH genetic disease; INTERACTS WITH bisphenol A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: MAMDC2-AS2; SMC5 antisense RNA 1 (head to head); SMC5-AS1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38970,216,059 - 70,258,874 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl970,193,997 - 70,258,866 (-)EnsemblGRCh38hg38GRCh38
GRCh37972,830,975 - 72,873,790 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map9q21.12NCBI
HuRef942,670,903 - 42,713,547 (-)NCBIHuRef
CHM1_1972,977,474 - 73,020,319 (-)NCBICHM1_1
T2T-CHM13v2.0982,382,866 - 82,425,722 (-)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
bisphenol A  (EXP)

References
Additional References at PubMed
PMID:12477932   PMID:14702039  


Genomics

Variants

.
Variants in SMC5-DT
6 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q21.11-21.13(chr9:68454847-76252863)x1 copy number loss See cases [RCV000133632] Chr9:68454847..76252863 [GRCh38]
Chr9:71130848..78867779 [GRCh37]
Chr9:70259583..78057599 [NCBI36]
Chr9:9q21.11-21.13		 pathogenic
GRCh38/hg38 9p24.3-q21.12(chr9:193412-70630731)x3 copy number gain See cases [RCV000136152] Chr9:193412..70630731 [GRCh38]
Chr9:220253..73245647 [GRCh37]
Chr9:210253..72435467 [NCBI36]
Chr9:9p24.3-q21.12		 pathogenic
GRCh38/hg38 9p24.3-q21.13(chr9:193412-74615913)x3 copy number gain See cases [RCV000135954] Chr9:193412..74615913 [GRCh38]
Chr9:204193..77230829 [GRCh37]
Chr9:194193..76420649 [NCBI36]
Chr9:9p24.3-q21.13		 pathogenic
GRCh38/hg38 9q21.11-31.2(chr9:68420430-106579493)x3 copy number gain See cases [RCV000136788] Chr9:68420430..106579493 [GRCh38]
Chr9:71130848..109341774 [GRCh37]
Chr9:70225166..108381595 [NCBI36]
Chr9:9q21.11-31.2		 pathogenic
GRCh38/hg38 9q21.11-21.12(chr9:68420349-70939579)x1 copy number loss See cases [RCV000137529] Chr9:68420349..70939579 [GRCh38]
Chr9:71130848..73554495 [GRCh37]
Chr9:70225085..72744315 [NCBI36]
Chr9:9q21.11-21.12		 likely pathogenic
GRCh38/hg38 9q21.11-21.32(chr9:68499530-83670227)x1 copy number loss See cases [RCV000137963] Chr9:68499530..83670227 [GRCh38]
Chr9:71130848..86285142 [GRCh37]
Chr9:70304266..85474962 [NCBI36]
Chr9:9q21.11-21.32		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
GRCh38/hg38 9q21.12-31.3(chr9:69627642-111454304)x3 copy number gain See cases [RCV000139789] Chr9:69627642..111454304 [GRCh38]
Chr9:72242558..114216584 [GRCh37]
Chr9:71432378..113256405 [NCBI36]
Chr9:9q21.12-31.3		 pathogenic
GRCh38/hg38 9p24.3-q22.1(chr9:203861-88130444)x4 copy number gain See cases [RCV000141904] Chr9:203861..88130444 [GRCh38]
Chr9:203861..90745359 [GRCh37]
Chr9:193861..89935179 [NCBI36]
Chr9:9p24.3-q22.1		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q21.31(chr9:193412-79877816)x3 copy number gain See cases [RCV000143012] Chr9:193412..79877816 [GRCh38]
Chr9:204104..82492731 [GRCh37]
Chr9:194104..81682551 [NCBI36]
Chr9:9p24.3-q21.31		 pathogenic
GRCh38/hg38 9q21.11-21.13(chr9:68624483-72028837)x3 copy number gain See cases [RCV000143753] Chr9:68624483..72028837 [GRCh38]
Chr9:71239399..74643753 [GRCh37]
Chr9:70429219..73833573 [NCBI36]
Chr9:9q21.11-21.13		 likely pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124532)x3 copy number gain See cases [RCV000053745] Chr9:193412..138124532 [GRCh38]
Chr9:204193..141018984 [GRCh37]
Chr9:194193..140138805 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|See cases [RCV000053748] Chr9:193412..138179445 [GRCh38]
Chr9:266045..141073897 [GRCh37]
Chr9:256045..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
NM_153267.5(MAMDC2):c.1937T>C (p.Val646Ala) single nucleotide variant not provided [RCV000959068] Chr9:70225775 [GRCh38]
Chr9:72840691 [GRCh37]
Chr9:9q21.12		 benign
NM_153267.5(MAMDC2):c.1874G>A (p.Arg625Gln) single nucleotide variant not provided [RCV000885905] Chr9:70218559 [GRCh38]
Chr9:72833475 [GRCh37]
Chr9:9q21.12		 benign
NM_153267.5(MAMDC2):c.1721T>C (p.Leu574Pro) single nucleotide variant Inborn genetic diseases [RCV002689467] Chr9:70218406 [GRCh38]
Chr9:72833322 [GRCh37]
Chr9:9q21.12		 uncertain significance
NM_153267.5(MAMDC2):c.2000T>C (p.Met667Thr) single nucleotide variant Inborn genetic diseases [RCV002670184] Chr9:70225971 [GRCh38]
Chr9:72840887 [GRCh37]
Chr9:9q21.12		 uncertain significance
NM_153267.5(MAMDC2):c.2009C>G (p.Thr670Arg) single nucleotide variant Inborn genetic diseases [RCV002723509] Chr9:70225980 [GRCh38]
Chr9:72840896 [GRCh37]
Chr9:9q21.12		 uncertain significance
NM_153267.5(MAMDC2):c.1702C>T (p.Arg568Cys) single nucleotide variant Inborn genetic diseases [RCV003207164] Chr9:70218387 [GRCh38]
Chr9:72833303 [GRCh37]
Chr9:9q21.12		 uncertain significance
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:192
Count of miRNA genes:153
Interacting mature miRNAs:155
Transcripts:ENST00000594708
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.

Markers in Region
STS-N33222  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37972,808,970 - 72,809,103UniSTSGRCh37
GRCh3710112,848,258 - 112,848,849UniSTSGRCh37
Build 36971,998,790 - 71,998,923RGDNCBI36
Celera10106,579,860 - 106,580,451UniSTS
Celera943,399,365 - 43,399,498RGD
Cytogenetic Map9q21.12UniSTS
HuRef942,648,891 - 42,649,024UniSTS
GeneMap99-GB4 RH Map9243.79UniSTS
NCBI RH Map9656.8UniSTS
RH47183  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37972,832,191 - 72,832,357UniSTSGRCh37
GRCh37642,924,220 - 42,924,386UniSTSGRCh37
Build 36643,032,198 - 43,032,364RGDNCBI36
Celera943,422,586 - 43,422,752UniSTS
Celera644,476,485 - 44,476,651RGD
Cytogenetic Map6p21.1UniSTS
Cytogenetic Map3q12UniSTS
Cytogenetic Map9q21.11UniSTS
Cytogenetic Map9q21.12UniSTS
HuRef942,672,119 - 42,672,285UniSTS
HuRef642,641,527 - 42,641,693UniSTS
GeneMap99-GB4 RH Map6155.42UniSTS
D11S3014  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2q14.1UniSTS
Cytogenetic Map2p16.1UniSTS
Cytogenetic Map16p13.12UniSTS
Cytogenetic Map15q21UniSTS
Cytogenetic MapXq22.3UniSTS
Cytogenetic Map18q21.33UniSTS
Cytogenetic Map2p15UniSTS
Cytogenetic Map21q21.2UniSTS
Cytogenetic Map14q32.13UniSTS
Cytogenetic Map14q23.1UniSTS
Cytogenetic Map18q23UniSTS
Cytogenetic Map15q25.2UniSTS
Cytogenetic Map6q25.1UniSTS
Cytogenetic Map3q21.1UniSTS
Cytogenetic Map8p21.1UniSTS
Cytogenetic Map12q23.1UniSTS
Cytogenetic Map12p12.1UniSTS
Cytogenetic Map12q24.11UniSTS
D11S3026  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map9q31.1UniSTS
Cytogenetic Map2p15UniSTS
Cytogenetic Map1q41UniSTS
Cytogenetic Map12p12.1UniSTS
Cytogenetic Map6q25.1UniSTS
Cytogenetic Map12q21.32UniSTS
Cytogenetic Map14q23.1UniSTS
D11S3076  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2q33-q34UniSTS
Cytogenetic MapXq22.3UniSTS
Cytogenetic Map2q22-q23UniSTS
Cytogenetic Map2p16.1UniSTS
Cytogenetic Map2q13UniSTS
Cytogenetic Map14q13.3UniSTS
Cytogenetic Map4pUniSTS
Cytogenetic Map6q12UniSTS
D3S3184  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map9q33.1UniSTS
Cytogenetic Map3p12.1UniSTS
Cytogenetic Map2q13UniSTS
DXS7960   No map positions available.
D11S2442  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map1p22.3UniSTS
Cytogenetic MapXq22.3UniSTS
Cytogenetic Map2q32.1UniSTS
Cytogenetic Map14q32.13UniSTS
Cytogenetic MapXq13.2-q21.1UniSTS
Cytogenetic Map6q12UniSTS
Cytogenetic Map2q13UniSTS
Cytogenetic Map14q13.3UniSTS
Cytogenetic Map12q23.1UniSTS
Cytogenetic Map18q23UniSTS
D11S3243  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map3p12.1UniSTS
D11S3553  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map10q11.2UniSTS
Cytogenetic Map3p12.1UniSTS
Cytogenetic Map2q13UniSTS
Cytogenetic Map9q33.1UniSTS


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 3 11 4
Low 2271 1536 1392 436 752 279 2886 984 2016 380 1397 1556 169 630 1833 4
Below cutoff 158 1210 325 183 918 182 1453 1187 1680 35 39 48 1 572 943

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000594708
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl970,193,997 - 70,258,866 (-)Ensembl
RefSeq Acc Id: ENST00000656832
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl970,216,085 - 70,258,866 (-)Ensembl
RefSeq Acc Id: ENST00000664022
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl970,194,058 - 70,229,311 (-)Ensembl
RefSeq Acc Id: ENST00000670800
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl970,228,990 - 70,258,822 (-)Ensembl
RefSeq Acc Id: ENST00000685052
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl970,228,993 - 70,258,810 (-)Ensembl
RefSeq Acc Id: NR_039990
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38970,216,059 - 70,258,874 (-)NCBI
GRCh37972,830,975 - 72,873,790 (-)NCBI
HuRef942,670,903 - 42,713,547 (-)NCBI
CHM1_1972,977,474 - 73,020,319 (-)NCBI
T2T-CHM13v2.0982,382,866 - 82,425,722 (-)NCBI
Sequence:
Promoters
RGD ID:15096314
Promoter ID:EPDNEWNC_H1153
Type:initiation region
Name:SMC5-AS1_1
Description:SMC5 antisense RNA 1 (head to head) [Source:HGNCSymbol;Acc:HGNC:48718]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38970,258,855 - 70,258,915EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC SMC5-DT COSMIC
Ensembl Genes ENSG00000268364 Ensembl
GTEx ENSG00000268364 GTEx
HGNC ID HGNC:48718 ENTREZGENE
Human Proteome Map SMC5-DT Human Proteome Map
NCBI Gene SMC5-AS1 ENTREZGENE
RNAcentral URS000075E31F RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-10-19 SMC5-DT  SMC5 divergent transcript  SMC5-AS1  SMC5 antisense RNA 1 (head to head)  Symbol and/or name change 19259463 PROVISIONAL