Advanced Search (OLGA)

Gene: Supt4h1 (SPT4 homolog, DSIF elongation factor subunit) Ictidomys tridecemlineatus

Analyze

Symbol:

Supt4h1

Name:

SPT4 homolog, DSIF elongation factor subunit

RGD ID:

12668524

Description:

ENCODES a protein that exhibits protein heterodimerization activity (inferred); RNA polymerase II complex binding (inferred); zinc ion binding (inferred); INVOLVED IN negative regulation of transcription elongation by RNA polymerase II (ortholog); PARTICIPATES IN RNA polymerase I transcription pathway; RNA polymerase II transcription elongation pathway; ASSOCIATED WITH hereditary breast ovarian cancer syndrome (ortholog); intellectual disability (ortholog); Joubert syndrome 1 (ortholog); FOUND IN DSIF complex (inferred); nucleoplasm (inferred); nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

transcription elongation factor SPT4

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405602	32,320,496 - 32,330,835 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936490	4,744,443 - 4,749,868 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936490	4,744,307 - 4,751,043 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

hereditary breast ovarian cancer syndrome (ISO)

intellectual disability (ISO)

Joubert syndrome 1 (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

negative regulation of DNA-templated transcription, elongation (IEA)

negative regulation of transcription by RNA polymerase II (IEA)

negative regulation of transcription elongation by RNA polymerase II (IEA,ISO)

positive regulation of DNA-templated transcription, elongation (IEA)

positive regulation of transcription by RNA polymerase II (IEA)

regulation of DNA-templated transcription (IEA)

regulation of transcription elongation by RNA polymerase II (IEA)

transcription elongation by RNA polymerase II (IEA)

transcription elongation-coupled chromatin remodeling (IEA)

Cellular Component

DSIF complex (IEA)

nucleoplasm (IEA)

nucleus (IEA)

Molecular Function

protein binding (ISO)

protein heterodimerization activity (IEA)

RNA polymerase II complex binding (IEA)

zinc ion binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

RNA polymerase I transcription pathway (ISO)

RNA polymerase II transcription elongation pathway (ISO)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Supt4h1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405602	32,320,496 - 32,330,835 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936490	4,744,443 - 4,749,868 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936490	4,744,307 - 4,751,043 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SUPT4H1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	17	58,345,178 - 58,352,201 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	17	58,345,175 - 58,353,093 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	17	56,422,539 - 56,429,562 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	53,777,538 - 53,784,562 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	17	53,777,537 - 53,784,562	NCBI
Celera	17	52,884,325 - 52,891,352 (-)	NCBI		Celera
Cytogenetic Map	17	q22	NCBI
HuRef	17	51,783,156 - 51,790,227 (-)	NCBI		HuRef
CHM1_1	17	56,487,550 - 56,494,613 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	17	59,213,053 - 59,220,076 (-)	NCBI		T2T-CHM13v2.0

Supt4a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	87,628,377 - 87,634,449 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	11	87,628,378 - 87,634,449 (+)	Ensembl		GRCm39 Ensembl
GRCm38	11	87,737,551 - 87,743,623 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	87,737,552 - 87,743,623 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	87,551,067 - 87,557,119 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	11	87,553,760 - 87,559,812 (+)	NCBI		MGSCv36	mm8
Celera	11	97,333,101 - 97,339,153 (+)	NCBI		Celera
Cytogenetic Map	11	C	NCBI
cM Map	11	52.2	NCBI

Supt4h1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	10	73,036,560 - 73,042,821 (+)	NCBI		GRCr8
mRatBN7.2	10	72,539,323 - 72,545,582 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	72,539,382 - 72,545,831 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	77,149,795 - 77,156,042 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	10	76,654,742 - 76,660,989 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	10	72,119,248 - 72,125,495 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	10	75,032,365 - 75,038,547 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	75,032,365 - 75,038,547 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	75,063,841 - 75,070,023 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	76,030,806 - 76,036,988 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	10	76,045,182 - 76,051,065 (+)	NCBI
Celera	10	71,452,699 - 71,458,881 (+)	NCBI		Celera
Cytogenetic Map	10	q26	NCBI

Supt4h1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955451	4,682,311 - 4,688,008 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955451	4,682,308 - 4,688,008 (+)	NCBI	ChiLan1.0	ChiLan1.0

SUPT4H1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	19	74,516,257 - 74,523,264 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	17	79,327,422 - 79,334,435 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	17	52,420,503 - 52,427,514 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	17	57,276,028 - 57,282,516 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

SUPT4H1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	32,990,060 - 32,996,023 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	32,990,061 - 33,191,176 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	32,227,026 - 32,233,008 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	33,796,673 - 33,802,638 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	9	33,796,674 - 33,802,664 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	9	32,582,834 - 32,588,782 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	32,866,332 - 32,872,298 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	32,959,764 - 32,965,781 (-)	NCBI		UU_Cfam_GSD_1.0

SUPT4H1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	34,619,729 - 34,629,646 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	34,622,775 - 34,629,681 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	36,183,672 - 36,193,623 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SUPT4H1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	16	35,047,874 - 35,054,438 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	16	35,047,934 - 35,054,239 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666077	5,862,496 - 5,869,211 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Supt4h1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624871	184,298 - 189,798 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624871	183,495 - 189,838 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_021724011	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000662	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000036229 ⟹ ENSSTOP00000031032

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936490	4,744,443 - 4,749,868 (+)	Ensembl

RefSeq Acc Id:

XM_021724011 ⟹ XP_021579686

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024405602	32,320,496 - 32,330,835 (-)	NCBI
SpeTri2.0	NW_004936490	4,744,307 - 4,751,043 (+)	NCBI

Sequence:

show sequence

GCGGGGCCGGCGCCCTCCTACACCGGAAGAGGAAGTCGGGCCCCAGAAGTGACAGGCATTCTGG
GTAGTGAGCTGTTTACTTCCTGCGGTGTGGAGGCTGTGGTCGTGTACCCTGCTGTTCTTCGAAT
CCGAGAGGATGGCTTTGGAGACTGTGCCCAAGGACCTGCGGCATCTGCGAGCTTGTCTGCTGTG
TTCGCTGGTCAAGACAATAGACCAGTTTGAATATGACGGTTGTGATAATTGTGATGCATACCTA
CAAATGAAGGGTAATCGAGAGATGGTATATGACTGCACCAGCTCTTCCTTTGATGGGAATGGAC
CTTTCTTCGCCTACTATATCTTCCCTCACAGAGCTGTTTCTTTTCTTGCCACAGGAATTGTGCG
AGAGCTGAAAAGTCGAGGAGTGGCCTACAAATCCAGAGACACGGCTATAAAAACCTAGCAAGAT
TCAGGCTGCCAGCATCTTTTCAGTCCACCTCCTTCCTCTGCTTATTTTTTGTTGTGGAACTAAA
CAGGCAGAACTTCAAATACTACTTGCCCTCCAACTCTGAGAATGAACAGACAATTGAGAGATTG
TCTGTCTCCACCATTTCACCTTGGGATAGTGGTGGAGGTGGAGGGGTTGGGGCTGGAGGGTTCA
CAGAGACTGAATTGAGGAGAAAGGATGCTGGTATTCCTGCTCACACCCTGGGCTGTGCTTTTGC
CCATGGGCAGTACTTTGAGTTAAATTCCAATTAACATGAACCACTGGAAAATTCTTAAAACTAT
GACACATGGCTTACCTCCCTCTCCCTTTCTTTCAGCTAGGCACAATAAGGGCTCACTTGCCTGG
TAAGCACCATCCAACACAATAAAGGCTCTTCTGCTCTTGTCACCTGTTTCTGGGCCTCCAGAAG
TCAGCCTTCCCACCATACTTGCTTGAGTTTCATTGGAAGGTCTGCTGTTCTGTGGCACAGTAAC
CTCTCAGTGTAGTCCCACTGTCTAGTGCTTATGTCTTGCCCTCTAGACCTGTCATATCAGTCTC
TTGAAATCTTGAGGCTTAGTGTTCTTTGCTCCTTGACTTTGTTCAATACTGCTTCTTTTCCTTC
TTTGTCTCTTTATATTTACTGATCTACCTATAACTTTGGCTAGTCTCATCGTCATTTTACATTC
CCCTCTGGAGACCTTCCAGCCTCAGGTGGGTCTTGTCTGGAAGTTTGTGCCTCTGTGGGAAGTT
GGCTTTGCCTTCTCTAACTTGGTAGGGTGCTTTGGGTAATTACAAGGGCCAAGGTGAGTTACCT
GTTTTAAAATTTAAAAATTACCATAAACTCATTTATTTAAGTTTCCACAGAAATCCTATTAGTA
TCCCCATTTTGATTTAAGTTCATCCATAAAGTGACTTAAGTGATTATACTCTATTTACTTCAAG
ATTCTTGTGATCAGAAATGAAGCAATGTGCTAGGCATGGTGGCACATGTTATAATGAGGCAGGA
GGATCACAGGTTCAAAGTCAGCCTCAGCAACTTAGGTTGTAAGCTACCTAGTGAGACCCTGTCT
CAAAATGAAAAATAAAAGGCTAGGCACGTGGCCCAATGGTTAGGCACACTTTGGTTCAACCTCT
GGAACCAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_021579686	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000031032.1
GenBank Protein	KAG3269353	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	XP_021579686 ⟸ XM_021724011
- Sequence:	show sequence MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGNGPFF AYYIFPHRAVSFLATGIVRELKSRGVAYKSRDTAIKT hide sequence

Ensembl Acc Id:

ENSSTOP00000031032 ⟸ ENSSTOT00000036229

Protein Domains

Spt4/RpoE2 zinc finger

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000032338	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000036229.1	UniProtKB/TrEMBL
Gene3D-CATH	3.30.40.210	UniProtKB/TrEMBL
InterPro	RPABC4/Spt4	UniProtKB/TrEMBL
	Spt4	UniProtKB/TrEMBL
	Spt4/RpoE2_Znf	UniProtKB/TrEMBL
	Spt4_sf	UniProtKB/TrEMBL
NCBI Gene	Supt4h1	ENTREZGENE
PANTHER	PTHR12882	UniProtKB/TrEMBL
	TRANSCRIPTION ELONGATION FACTOR SPT4	UniProtKB/TrEMBL
Pfam	Spt4	UniProtKB/TrEMBL
SMART	Spt4	UniProtKB/TrEMBL
Superfamily-SCOP	SSF63393	UniProtKB/TrEMBL
UniProt	A0A287DBT4_ICTTR	UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

RGD Manual Annotations

Send us a Message

Imported Disease Annotations - ClinVar

RGD Manual Annotations