SUPT4H1 (SPT4 homolog, DSIF elongation factor subunit)

Gene: SUPT4H1 (SPT4 homolog, DSIF elongation factor subunit) Sus scrofa

Analyze

Symbol:

SUPT4H1

Name:

SPT4 homolog, DSIF elongation factor subunit

RGD ID:

14109626

Description:

ENCODES a protein that exhibits protein heterodimerization activity (inferred); RNA polymerase II complex binding (inferred); translation elongation factor activity (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 genetic disease (ortholog); intellectual disability (ortholog); Joubert syndrome 1 (ortholog); FOUND IN DSIF complex (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

transcription elongation factor SPT4

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

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

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

intellectual disability (ISO)

Joubert syndrome 1 (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chromatin organization (IEA)

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)

translational elongation (IEA)

Cellular Component

DSIF complex (IEA,ISO)

nucleoplasm (IEA)

nucleus (IEA)

Molecular Function

protein binding (ISO)

protein heterodimerization activity (IEA)

RNA polymerase II complex binding (IEA)

translation elongation factor activity (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:15679890	PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

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
(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
(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
(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

Variants

Variants in SUPT4H1
203 total Variants

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	hemolymphoid system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system
High
Medium	8	2		5		1			3
Low	2	2	3		2	22	2	3
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_003131646	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000080	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK400066	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY610383	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CU681830	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GFLN01119601	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSSCT00000045227 ⟹ ENSSSCP00000037058

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1 Ensembl	12	34,619,729 - 34,629,646 (-)	Ensembl

RefSeq Acc Id:

XM_003131646 ⟹ XP_003131694

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	12	34,622,775 - 34,629,681 (-)	NCBI

Sequence:

show sequence

GGAAGTGCGTGTATTCTGGGCAAATCGCTGTTTACTTCCTGCGAGCGGCAGCTGTGGCTCATTC
CGTCGCTGTTCTTCCTTGGAAGAGGATGGCTCTGGAGACAGTGCCGAAGGACCTGCGGCATCTG
CGCGCTTGTTTGCTGTGTTCGCTGGTCAAGACTATAGACCAGTTTGAATATGATGGTTGTGACA
ATTGTGATGCATACCTTCAGATGAAAGGTAACCGAGAGATGGTATATGACTGCACCAGCTCTTC
CTTTGATGGAATCATTGCAATGATGAGTCCAGAGGACAGCTGGGTCTCCAAGTGGCAGCGAGTC
AGTAACTTTAAGCCGGGGGTATATGCAGTGTCAGTCACAGGTCGCCTTCCCCAAGGAATCGTGC
GGGAGCTGAAAAGTCGAGGAGTGGCCTACAAATCCAGAGACACAGCTATAAAGACCTAGCGAGA
TGCACAGCCTCCAGCATCTTTGTTCCTGCCTCTGCCTCTGCCCCTGCTTATTTTTTGTTGTGGA
ACTAAATGGGCAGAACTGCAAATACGTCCCACCCTCCGAGTCTGAGACTCAGGCTGTTGAGGGA
GCAGCACAGTGTGTCCATGGGCCGTTTTACCTTCTCTGGTGGACTGCGGCAAGGATGGGAGCAG
TTTGGGCTGGTGGAGTGACAGAGACTGAATTCAGTGGGGACTAGGATACTGGTTTTCCTACCCA
CCACTCAGAGCTGTGCCCTTGCTCTTGCCCTTGGGCAGGACTCTGGGTCAAACGCAAATAAACA
TGAACCCCGTAGGGCTATTCTTAAGGCTGTAACAAATGCCTCCTCTCCCTCTTCCTTTTTCTTA
GCTGGGCACAGTCAAAACTCATTGCCCAGTAAGCATCTTCCCAGATCAGCAGAGGCCCTGCAGG
CCGCTCCCTGCAGCCTTCCCAGTGTGCTTCCTTGGGTCTCAGGAGGTCTGCTGTCCGAGTCTAG
GCAGCCCTCAGCCTGGTAGTCCTGGTGTGTCTGCTGGTTGTAACTTTCCCTTCTCTAGATCTGG
CTCAGTGGGTGTCCCTCAAAGAAATCCTGGGCCGCCTTCCTGTTCTTTGCCCCTTGACCACATT
TAGAACCTTTTTTCCGTCTTTGTTGTTTTTTTTTTTTTTTTTTACTGTCCTTCCTACACCTTAG
GTCCACCAGTGGCACCCATGATCTCCCTCTCCCCTGCTTTCCTGCGTTTCCCTAATGGAGACCC
TCAGGTTGCCGATGGGTCTTGGTCTGGCTCCTCTATCCCTCCGCAGGAGGTGGGCTCTCCTCTC
TCTGACCTAGCGGGGGGCCTTGAGTGATGTCCAGTTAGTGGCCAAGGTGAGTGACTTGTTTTGG
AATTAAATTTTTTACCGTTAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_003131694	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSSCP00000037058
	ENSSSCP00000037058.3
	ENSSSCP00005017764.1
	ENSSSCP00015009917.1
	ENSSSCP00025015046.1
	ENSSSCP00030044568.1
	ENSSSCP00035035117.1
	ENSSSCP00040009591.1
	ENSSSCP00045017983.1
	ENSSSCP00050022044.1
	ENSSSCP00055031622.1
	ENSSSCP00060034498.1
	ENSSSCP00065016937.1
	ENSSSCP00070003236.1
	ENSSSCP00070003242.1

RefSeq Acc Id:	XP_003131694 ⟸ XM_003131646
- UniProtKB:	A0A286ZZX0 (UniProtKB/TrEMBL), A0A4X1SL69 (UniProtKB/TrEMBL), A0A480VIE8 (UniProtKB/TrEMBL), A0A4X1SLD9 (UniProtKB/TrEMBL), A0A8D0MWB4 (UniProtKB/TrEMBL)
- Sequence:	show sequence MALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMM SPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRDTAIKT hide sequence

RefSeq Acc Id:

ENSSSCP00000037058 ⟸ ENSSSCT00000045227

Protein Domains

Spt4/RpoE2 zinc finger

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSSCG00000034752	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSSSCG00005018410	UniProtKB/TrEMBL
	ENSSSCG00015019193	UniProtKB/TrEMBL
	ENSSSCG00025026633	UniProtKB/TrEMBL
	ENSSSCG00030069073	UniProtKB/TrEMBL
	ENSSSCG00035062803	UniProtKB/TrEMBL
	ENSSSCG00040016965	UniProtKB/TrEMBL
	ENSSSCG00045015365	UniProtKB/TrEMBL
	ENSSSCG00050038931	UniProtKB/TrEMBL
	ENSSSCG00055020250	UniProtKB/TrEMBL
	ENSSSCG00060058407	UniProtKB/TrEMBL
	ENSSSCG00065029713	UniProtKB/TrEMBL
	ENSSSCG00070002094	UniProtKB/TrEMBL
Ensembl Transcript	ENSSSCT00000045227	ENTREZGENE
	ENSSSCT00000045227.3	UniProtKB/TrEMBL
	ENSSSCT00005029110.1	UniProtKB/TrEMBL
	ENSSSCT00015025379.1	UniProtKB/TrEMBL
	ENSSSCT00025036040.1	UniProtKB/TrEMBL
	ENSSSCT00030096667.1	UniProtKB/TrEMBL
	ENSSSCT00035084422.1	UniProtKB/TrEMBL
	ENSSSCT00040022863.1	UniProtKB/TrEMBL
	ENSSSCT00045026051.1	UniProtKB/TrEMBL
	ENSSSCT00050052500.1	UniProtKB/TrEMBL
	ENSSSCT00055039754.1	UniProtKB/TrEMBL
	ENSSSCT00060079674.1	UniProtKB/TrEMBL
	ENSSSCT00065040082.1	UniProtKB/TrEMBL
	ENSSSCT00070003908.1	UniProtKB/TrEMBL
	ENSSSCT00070003915.1	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
KEGG Report	ssc:100515097	UniProtKB/TrEMBL
NCBI Gene	SUPT4H1	ENTREZGENE
PANTHER	PTHR12882	UniProtKB/TrEMBL
	TRANSCRIPTION ELONGATION FACTOR SPT4	UniProtKB/TrEMBL
Pfam	Spt4	UniProtKB/TrEMBL
PIRSF	Spt4	UniProtKB/TrEMBL
SMART	Spt4	UniProtKB/TrEMBL
Superfamily-SCOP	SSF63393	UniProtKB/TrEMBL
UniProt	A0A286ZZX0	ENTREZGENE
	A0A480VIE8	ENTREZGENE, UniProtKB/TrEMBL
	A0A4X1SL69	ENTREZGENE, UniProtKB/TrEMBL
	A0A4X1SLD9	ENTREZGENE, UniProtKB/TrEMBL
	A0A8D0MWB4	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	A0A286ZZX0	UniProtKB/TrEMBL
VGNC ID	VGNC:93624	ENTREZGENE

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