Supt20hl1 (Supt20h like 1) - Rat Genome Database

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Gene: Supt20hl1 (Supt20h like 1) Rattus norvegicus
Analyze
Symbol: Supt20hl1 (Ensembl: LOC367830)
Name: Supt20h like 1 (Ensembl:similar to FAM48A protein)
RGD ID: 1563909
Description: Predicted to enable transcription coregulator activity. Predicted to be part of SAGA complex; INTERACTS WITH bisphenol A (ortholog); valproic acid (ortholog).
Type: protein-coding
RefSeq Status: PREDICTED
Previously known as: hypothetical protein LOC367830; LOC367830; MGC114387; similar to FAM48A protein; uncharacterized protein LOC367830
RGD Orthologs
Human
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X62,702,311 - 62,752,762 (+)NCBIGRCr8
mRatBN7.2X58,708,504 - 58,758,962 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX58,708,504 - 58,758,960 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX60,146,077 - 60,196,549 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X63,647,199 - 63,697,670 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X61,198,112 - 61,248,642 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X63,064,950 - 63,115,272 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX63,064,950 - 63,115,272 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X63,654,885 - 63,705,065 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X81,333,010 - 81,383,745 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX59,144,837 - 59,195,174 (+)NCBICelera
Cytogenetic MapXq22NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
SAGA complex  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Comparative Map Data
Supt20hl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X62,702,311 - 62,752,762 (+)NCBIGRCr8
mRatBN7.2X58,708,504 - 58,758,962 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX58,708,504 - 58,758,960 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX60,146,077 - 60,196,549 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X63,647,199 - 63,697,670 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X61,198,112 - 61,248,642 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X63,064,950 - 63,115,272 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX63,064,950 - 63,115,272 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X63,654,885 - 63,705,065 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X81,333,010 - 81,383,745 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX59,144,837 - 59,195,174 (+)NCBICelera
Cytogenetic MapXq22NCBI
SUPT20HL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X24,360,639 - 24,367,839 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX24,360,639 - 24,367,839 (+)EnsemblGRCh38hg38GRCh38
GRCh37X24,378,756 - 24,385,956 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X24,290,331 - 24,336,420 (+)NCBINCBI36Build 36hg18NCBI36
CeleraX28,503,761 - 28,506,424 (+)NCBICelera
Cytogenetic MapXp22.11NCBI
HuRefX22,122,907 - 22,125,573 (+)NCBIHuRef
CHM1_1X24,411,915 - 24,414,575 (+)NCBICHM1_1
T2T-CHM13v2.0X23,944,797 - 23,952,006 (+)NCBIT2T-CHM13v2.0

Variants

.
Variants in Supt20hl1
85 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:61
Count of miRNA genes:54
Interacting mature miRNAs:60
Transcripts:ENSRNOT00000017923
Prediction methods:Miranda, Pita, Rnahybrid, Targetscan
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X5704214165612192Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat

Markers in Region
DXRat56  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X58,753,434 - 58,753,614 (+)MAPPERmRatBN7.2
Rnor_6.0X63,109,746 - 63,109,925NCBIRnor6.0
Rnor_5.0X63,699,539 - 63,699,718UniSTSRnor5.0
RGSC_v3.4X81,378,219 - 81,378,398UniSTSRGSC3.4
RGSC_v3.4X81,378,218 - 81,378,398RGDRGSC3.4
RGSC_v3.1X81,451,511 - 81,451,690RGD
CeleraX59,189,648 - 59,189,827UniSTS
RH 3.4 Map41029.5RGD
RH 3.4 Map41029.5UniSTS
FHH x ACI MapX21.8699RGD
FHH x ACI MapX21.8699UniSTS
Cytogenetic MapXq31UniSTS
Cytogenetic Map6q13UniSTS


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 endocrine system hemolymphoid system reproductive system
High
Medium
Low 39
Below cutoff 5 13 11 67

Sequence


Ensembl Acc Id: ENSRNOT00000017923
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX58,708,504 - 58,758,960 (+)Ensembl
Rnor_6.0 EnsemblX63,064,950 - 63,115,272 (+)Ensembl
RefSeq Acc Id: NM_001037211   ⟹   NP_001032288
RefSeq Status: PREDICTED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X62,702,311 - 62,752,762 (+)NCBI
mRatBN7.2X58,708,504 - 58,758,962 (+)NCBI
Rnor_6.0X63,064,950 - 63,115,272 (+)NCBI
Rnor_5.0X63,654,885 - 63,705,065 (+)NCBI
RGSC_v3.4X81,333,010 - 81,383,745 (+)RGD
CeleraX59,144,837 - 59,195,174 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032288 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI00150 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000076554.1
RefSeq Acc Id: NP_001032288   ⟸   NM_001037211
- UniProtKB: Q498N0 (UniProtKB/TrEMBL)
- Sequence:
Protein Domains
Spt20-like SEP

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-2251 BioCyc
Ensembl Genes ENSRNOG00000042530 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017923.7 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7442108 IMAGE-MGC_LOAD
InterPro Spt20 UniProtKB/TrEMBL
  Spt20-like_SEP UniProtKB/TrEMBL
KEGG Report rno:367830 UniProtKB/TrEMBL
MGC_CLONE MGC:114387 IMAGE-MGC_LOAD
NCBI Gene 367830 ENTREZGENE
PANTHER PTHR13526 UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR SPT20 HOMOLOG UniProtKB/TrEMBL
Pfam Spt20 UniProtKB/TrEMBL
PhenoGen Supt20hl1 PhenoGen
RatGTEx ENSRNOG00000042530 RatGTEx
UniProt Q498N0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Supt20hl1  Supt20h like 1  LOC367830  similar to FAM48A protein  Symbol and Name Changed 1299863 APPROVED
2006-02-09 LOC367830  similar to FAM48A protein      Symbol and Name status set to provisional 70820 PROVISIONAL