SAP30-DT (SAP30 divergent transcript) - Rat Genome Database

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Gene: SAP30-DT (SAP30 divergent transcript) Homo sapiens
Analyze
Symbol: SAP30-DT
Name: SAP30 divergent transcript
RGD ID: 14700586
HGNC Page HGNC:54424
Description: INTERACTS WITH acrylamide; sotorasib; trametinib
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC124900813; MIRE; uncharacterized LOC124900813
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384173,349,231 - 173,370,698 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4173,349,543 - 173,370,721 (-)EnsemblGRCh38hg38GRCh38
Cytogenetic Map4q34.1NCBI
CHM1_14174,261,378 - 174,268,642 (-)NCBICHM1_1
T2T-CHM13v2.04176,688,654 - 176,710,098 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
acrylamide  (EXP)
sotorasib  (EXP)
trametinib  (EXP)

References
Additional References at PubMed
PMID:31330194   PMID:37248433  


Genomics

Variants

.
Variants in SAP30-DT
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q32.2-35.2(chr4:162013220-189975519)x3 copy number gain See cases [RCV000050649] Chr4:162013220..189975519 [GRCh38]
Chr4:162934372..190828225 [GRCh37]
Chr4:163153822..191133668 [NCBI36]
Chr4:4q32.2-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:165281036-190018185)x1 copy number loss See cases [RCV000140414] Chr4:165281036..190018185 [GRCh38]
Chr4:166202188..190939340 [GRCh37]
Chr4:166421638..191176334 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:166317587-190095391)x1 copy number loss See cases [RCV000137532] Chr4:166317587..190095391 [GRCh38]
Chr4:167238739..190828225 [GRCh37]
Chr4:167458189..191250527 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:172501374-190095332)x1 copy number loss See cases [RCV000143079] Chr4:172501374..190095332 [GRCh38]
Chr4:173422525..190828225 [GRCh37]
Chr4:173659100..191250468 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q31.1-35.2(chr4:138510532-189963195)x3 copy number gain See cases [RCV000136810] Chr4:138510532..189963195 [GRCh38]
Chr4:139431686..190828225 [GRCh37]
Chr4:139651136..191121344 [NCBI36]
Chr4:4q31.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-34.3(chr4:166630207-179820960) copy number loss See cases [RCV000141653] Chr4:166630207..179820960 [GRCh38]
Chr4:167551358..180742113 [GRCh37]
Chr4:167770808..180979107 [NCBI36]
Chr4:4q32.3-34.3		 pathogenic
GRCh38/hg38 4q33-35.2(chr4:169901205-190095391)x3 copy number gain See cases [RCV000138540] Chr4:169901205..190095391 [GRCh38]
Chr4:170822356..190828225 [GRCh37]
Chr4:171058931..191250527 [NCBI36]
Chr4:4q33-35.2		 uncertain significance
GRCh38/hg38 4q32.3-35.2(chr4:168970400-186936738)x1 copy number loss See cases [RCV000142368] Chr4:168970400..186936738 [GRCh38]
Chr4:169891551..187857892 [GRCh37]
Chr4:170128126..188094886 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)x1 copy number loss See cases [RCV000141964] Chr4:167373716..190036318 [GRCh38]
Chr4:168294867..190957473 [GRCh37]
Chr4:168531442..191194467 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:164039530-189982708)x1 copy number loss See cases [RCV000053347] Chr4:164039530..189982708 [GRCh38]
Chr4:164960682..190828225 [GRCh37]
Chr4:165180132..191140857 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:171507704-189869726)x1 copy number loss See cases [RCV000053349] Chr4:171507704..189869726 [GRCh38]
Chr4:172428855..190790881 [GRCh37]
Chr4:172665430..191027875 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q34.1-34.3(chr4:171851295-178772816)x1 copy number loss See cases [RCV000053350] Chr4:171851295..178772816 [GRCh38]
Chr4:172772446..179693970 [GRCh37]
Chr4:173009021..179930964 [NCBI36]
Chr4:4q34.1-34.3		 pathogenic
GRCh38/hg38 4q34.1-35.2(chr4:172356988-189975519)x1 copy number loss See cases [RCV000053352] Chr4:172356988..189975519 [GRCh38]
Chr4:173278139..190828225 [GRCh37]
Chr4:173514714..191133668 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q28.3-35.2(chr4:134935616-190036318)x3 copy number gain See cases [RCV000143559] Chr4:134935616..190036318 [GRCh38]
Chr4:135856771..190957473 [GRCh37]
Chr4:136076221..191194467 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic
GRCh38/hg38 4q28.1-35.1(chr4:125432943-185761887)x3 copy number gain See cases [RCV000138578] Chr4:125432943..185761887 [GRCh38]
Chr4:126354098..186683041 [GRCh37]
Chr4:126573548..186920035 [NCBI36]
Chr4:4q28.1-35.1		 pathogenic|likely benign
GRCh38/hg38 4q34.1-35.2(chr4:172200228-189975519)x3 copy number gain See cases [RCV000051804] Chr4:172200228..189975519 [GRCh38]
Chr4:173121379..190828225 [GRCh37]
Chr4:173357954..191133668 [NCBI36]
Chr4:4q34.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:168119317-190095391)x3 copy number gain See cases [RCV000143331] Chr4:168119317..190095391 [GRCh38]
Chr4:169040468..190828225 [GRCh37]
Chr4:169277043..191250527 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
GRCh38/hg38 4q31.21-35.2(chr4:145042668-189975519)x3 copy number gain See cases [RCV000135845] Chr4:145042668..189975519 [GRCh38]
Chr4:145963820..190828225 [GRCh37]
Chr4:146183270..191133668 [NCBI36]
Chr4:4q31.21-35.2		 pathogenic
GRCh38/hg38 4q28.3-35.2(chr4:131985253-190095391)x3 copy number gain See cases [RCV000137721] Chr4:131985253..190095391 [GRCh38]
Chr4:132906408..190828225 [GRCh37]
Chr4:133125858..191250527 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic|likely benign
GRCh38/hg38 4q33-35.2(chr4:169873508-190018185)x1 copy number loss See cases [RCV000140396] Chr4:169873508..190018185 [GRCh38]
Chr4:170794659..190939340 [GRCh37]
Chr4:171031234..191176334 [NCBI36]
Chr4:4q33-35.2		 pathogenic
GRCh38/hg38 4q33-35.2(chr4:170899124-190036318)x1 copy number loss See cases [RCV000143232] Chr4:170899124..190036318 [GRCh38]
Chr4:171820275..190957473 [GRCh37]
Chr4:172056850..191194467 [NCBI36]
Chr4:4q33-35.2		 pathogenic
GRCh38/hg38 4q34.1-34.3(chr4:171507504-181381327)x3 copy number gain See cases [RCV000051793] Chr4:171507504..181381327 [GRCh38]
Chr4:172428655..182302480 [GRCh37]
Chr4:172665230..182539474 [NCBI36]
Chr4:4q34.1-34.3		 pathogenic
GRCh38/hg38 4q27-35.2(chr4:121518223-190062270)x3 copy number gain See cases [RCV000051786] Chr4:121518223..190062270 [GRCh38]
Chr4:122439378..190828225 [GRCh37]
Chr4:122658828..191220419 [NCBI36]
Chr4:4q27-35.2		 pathogenic
GRCh38/hg38 4q26-35.2(chr4:118065569-190042639)x3 copy number gain See cases [RCV000051785] Chr4:118065569..190042639 [GRCh38]
Chr4:118986724..190828225 [GRCh37]
Chr4:119206172..191200788 [NCBI36]
Chr4:4q26-35.2		 pathogenic
GRCh38/hg38 4q32.1-35.2(chr4:160757699-190091407)x3 copy number gain See cases [RCV000140982] Chr4:160757699..190091407 [GRCh38]
Chr4:161678851..191012562 [GRCh37]
Chr4:161898301..191246543 [NCBI36]
Chr4:4q32.1-35.2		 pathogenic
GRCh38/hg38 4q31.22-34.1(chr4:147317283-173675559)x3 copy number gain See cases [RCV000051788] Chr4:147317283..173675559 [GRCh38]
Chr4:148238435..174596710 [GRCh37]
Chr4:148457885..174833285 [NCBI36]
Chr4:4q31.22-34.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:224
Count of miRNA genes:206
Interacting mature miRNAs:214
Transcripts:ENST00000608794, ENST00000608892, ENST00000609153, ENST00000609900
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 351 580 3 281 595 165 340 63 166 28 1 11 589
Low 2039 2108 1452 409 1420 251 3236 1451 3360 294 1266 1562 169 1193 1690 3
Below cutoff 40 292 268 213 243 213 523 574 8 61 15 18 508 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000608794
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,363,994 - 173,369,815 (-)Ensembl
RefSeq Acc Id: ENST00000608892
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,369,362 - 173,370,326 (-)Ensembl
RefSeq Acc Id: ENST00000609153
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,363,780 - 173,370,721 (-)Ensembl
RefSeq Acc Id: ENST00000609900
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,367,895 - 173,369,815 (-)Ensembl
RefSeq Acc Id: ENST00000651702
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,349,543 - 173,369,516 (-)Ensembl
RefSeq Acc Id: ENST00000658397
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,358,900 - 173,369,813 (-)Ensembl
RefSeq Acc Id: ENST00000666010
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4173,363,779 - 173,369,837 (-)Ensembl
RefSeq Acc Id: NR_183968
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384173,363,780 - 173,370,698 (-)NCBI
T2T-CHM13v2.04176,703,179 - 176,710,098 (-)NCBI
RefSeq Acc Id: NR_183969
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384173,363,780 - 173,370,698 (-)NCBI
T2T-CHM13v2.04176,703,179 - 176,710,098 (-)NCBI
RefSeq Acc Id: NR_183970
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384173,363,780 - 173,370,698 (-)NCBI
T2T-CHM13v2.04176,703,179 - 176,710,098 (-)NCBI
RefSeq Acc Id: NR_183971
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384173,366,188 - 173,370,698 (-)NCBI
T2T-CHM13v2.04176,705,587 - 176,710,098 (-)NCBI
RefSeq Acc Id: NR_183972
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384173,363,780 - 173,369,794 (-)NCBI
T2T-CHM13v2.04176,703,179 - 176,709,194 (-)NCBI
RefSeq Acc Id: NR_183973
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384173,349,231 - 173,370,698 (-)NCBI
T2T-CHM13v2.04176,688,654 - 176,710,098 (-)NCBI
RefSeq Acc Id: NR_183974
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384173,349,231 - 173,369,794 (-)NCBI
T2T-CHM13v2.04176,688,654 - 176,709,194 (-)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC SAP30-DT COSMIC
Ensembl Genes ENSG00000272870 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000609153 ENTREZGENE
  ENST00000666010 ENTREZGENE
GTEx ENSG00000272870 GTEx
HGNC ID HGNC:54424 ENTREZGENE
Human Proteome Map SAP30-DT Human Proteome Map
NCBI Gene SAP30-DT ENTREZGENE
RNAcentral URS0000D59DDA RNACentral
  URS00026A1A03 RNACentral
  URS00026A1D5E RNACentral
  URS00026A1D6A RNACentral
  URS00026A1FBB RNACentral
  URS00026A236B RNACentral
  URS00026A27A6 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-02-09 SAP30-DT  SAP30 divergent transcript  LOC124900813  uncharacterized LOC124900813  Data merged from RGD:151675879 737654 PROVISIONAL