H1-3 (H1.3 linker histone, cluster member)

Gene: H1-3 (H1.3 linker histone, cluster member) Chlorocebus sabaeus

Analyze

Symbol:

H1-3

Name:

H1.3 linker histone, cluster member

RGD ID:

18713664

Description:

ENCODES a protein that exhibits chromatin DNA binding (inferred); DNA binding (inferred); double-stranded DNA binding (inferred); INVOLVED IN chromatin organization (ortholog); negative regulation of transcription by RNA polymerase II (ortholog); regulation of transcription by RNA polymerase II (ortholog); FOUND IN chromatin (inferred); chromosome (inferred); euchromatin (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

histone H1.3

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

ChlSab1.1 - Green Monkey 1.1 Assembly

Position:

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	17	46,016,618 - 46,017,989 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	46,016,693 - 46,017,355 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666044	26,170,886 - 26,171,676 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chromatin organization (ISO)

chromosome condensation (IEA)

negative regulation of DNA recombination (IEA)

negative regulation of transcription by RNA polymerase II (ISO)

nucleosome assembly (IEA)

regulation of transcription by RNA polymerase II (ISO)

Cellular Component

chromatin (IEA)

chromosome (IEA)

euchromatin (IEA)

nucleosome (IEA)

nucleus (IEA)

Molecular Function

chromatin DNA binding (IEA)

DNA binding (IEA)

double-stranded DNA binding (IEA)

nucleosomal DNA binding (IEA)

protein binding (ISO)

structural constituent of chromatin (IEA)

References

Additional References at PubMed

PMID:22301074

Genomics

Comparative Map Data

H1-3
(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	17	46,016,618 - 46,017,989 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	46,016,693 - 46,017,355 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666044	26,170,886 - 26,171,676 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

H1-3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	26,234,212 - 26,234,987 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	26,234,212 - 26,234,987 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	26,234,440 - 26,235,215 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	26,342,419 - 26,343,195 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	6	26,342,418 - 26,343,195	NCBI
Celera	6	27,463,747 - 27,464,523 (-)	NCBI		Celera
Cytogenetic Map	6	p22.2	NCBI
HuRef	6	26,177,448 - 26,178,221 (-)	NCBI		HuRef
CHM1_1	6	26,236,600 - 26,237,376 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	26,102,677 - 26,103,452 (-)	NCBI		T2T-CHM13v2.0

H1f3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	23,739,206 - 23,739,981 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	13	23,737,436 - 23,744,860 (+)	Ensembl		GRCm39 Ensembl
GRCm38	13	23,555,032 - 23,555,807 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	23,553,262 - 23,560,686 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	13	23,646,901 - 23,649,877 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	13	23,562,499 - 23,565,473 (+)	NCBI		MGSCv36	mm8
Celera	13	23,786,995 - 23,789,971 (+)	NCBI		Celera
Cytogenetic Map	13	A3.1	NCBI
cM Map	13	9.79	NCBI

H4f3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	17	41,979,562 - 41,980,341 (-)	NCBI		GRCr8
mRatBN7.2	17	41,551,524 - 41,552,303 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	17	41,529,667 - 41,552,334 (-)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	17	43,797,711 - 43,798,450 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	17	43,797,721 - 43,798,383 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	17	45,652,308 - 45,655,450 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	17	41,182,415 - 41,183,154 (-)	NCBI		Celera
Cytogenetic Map	17	p11	NCBI

H1-3
(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	5	40,880,869 - 40,883,517 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	36,880,968 - 36,885,037 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	26,068,439 - 26,071,115 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	26,729,188 - 26,729,978 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	26,729,239 - 26,729,904 (-)	Ensembl	panpan1.1		panPan2

H1-3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	35	24,155,864 - 24,156,647 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	35	24,007,247 - 24,010,246 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	35	24,334,721 - 24,338,937 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	35	24,338,211 - 24,338,867 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	35	24,115,793 - 24,118,793 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	35	24,167,683 - 24,171,900 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	35	25,632,339 - 25,636,554 (-)	NCBI		UU_Cfam_GSD_1.0

H1-3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	7	20,881,642 - 20,882,307 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	22,072,582 - 22,075,157 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

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

	endocrine system	hemolymphoid system	nervous system
High
Medium		20	13
Low	1		27
Below cutoff	25		12

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_007973474	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACDXN010000012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCSAT00000019180 ⟹ ENSCSAP00000018600

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	17	46,016,693 - 46,017,355 (+)	Ensembl

RefSeq Acc Id:

XM_007973474 ⟹ XP_007971665

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	17	46,016,618 - 46,017,989 (+)	NCBI
Vero_WHO_p1.0	NW_023666044	26,170,886 - 26,171,676 (-)	NCBI

Sequence:

show sequence

CTCAGCCTCCGGCGCAGAGAACACGCCGTTCTGACAGTTTGAGATTACTTTTGTCTTTTCTGGC
AAAACAAAAACATGTCGGAGACTGCTCCAGTTGCTCCTATCACTCCTGCACCCGCAGAAAAAAT
ACCGGTGAAGAAAAAGGCGAAGAAGGCAGGCGCTACTGCTGGGAAACGCAAAGCATCCGGACCC
CCAGTGTCTGAGCTCATCACCAAGGCAGTGGCAGCTTCCAAAGAGCGCAGCGGCGTTTCTCTGG
CCGCGCTTAAGAAAGCGCTTGCGGCTGCTGGCTACGATGTAGAGAAAAACAACAGCCGTATCAA
GCTTGGCCTCAAGAGCTTGGTGAGCAAGGGTACTCTGGTGCAGACCAAAGGCACCGGTGCTTCT
GGATCCTTTAAACTGAACAAGAAAGCCGCTTCCGGGGAAGGCAAACCCAAGGCCAAGAAGGCTG
GCTCAGCCAAGCCTAGAAAGCCCGCTGCAGCAGCCAAGAAGCCCAAGAAAGCGAGTGGCGCCGC
TACCCCGAAGAAAAGCGTCAAAAAGACTCCTAAGAAGGCAAAGAAGCCAGCAACAGCTGCTGGG
ACCAAGAAAGTGGCCAAGAGTGCGAAAAAGGTGAAAACACCCCAGCCAAAAAAAGCCGCCAAGA
GTCCAGCTAAGGCCAAAGTCCCTAAGCCCAAGGCAGCCAAGCCTAAGTCGGCGAAGCCGAAGGT
TACAAAGGCAAAGAAGGCAGCTCCGAAGAAAAAGTGAAACTGGCGGGACGTTCCGCTTTGAAAA
TTTAAACGGCTCTTTTCAGAGCCACCCATAGGTCTCAGTCAAAAGAGCTGGCGCCTTTTTTGCG
GGGCCAGGGAGGCTGCGGGTGTGGTGTGCGGGCGCGGTCTATCCCAGCCATGCCGGTTGGGGTT
CAGTAACTCAGCTCCCAGCAGTCTGGGAGCAAGAATCCTTCCGCCTCAGCCACAGCCACCGGAG
TAGCTAAGGCTACTTGAACCACCAGGTTTTGCTTTTTCTTCAAATTCCCGCGGTGGTGTGTGAT
TGGCCGGCTGATTTCTCTCAAAGCGTGCGCTTAAAAGTGGCTCTGAAAAAATTTTATTCCTGGC
ACAGGGATATGGTGTAAATGCTTTAGTTTGCTTTAGCATTGAGGTGACTTCTTGAGCACAGCCT
GTCCTGGTTGTGAGCAGTACCTGGCATGCCTAAGGTTCCTGCGGCCCACCATCTTGTCCAGCGT
TGAAAATGGCCAACTGCAGGTGGCGCCCGCTGTCTGTCTTTTACAAGGCTTGTGAAACCCCTTA
GCTCTGGGATATGGGCCGTCAGGTACCGTACTTGGAAATAGGCAGTGTGGGCCTGCACTGCCTG
GCGAGGCGGCTCCCCTGTAATCCCAGCA

hide sequence

Protein Sequences


Protein RefSeqs	XP_007971665	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000018600.1

RefSeq Acc Id:	XP_007971665 ⟸ XM_007973474
- UniProtKB:	A0A0D9SCL1 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSCSAP00000018600 ⟸ ENSCSAT00000019180

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000019090	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000019180.1	UniProtKB/TrEMBL
Gene3D-CATH	1.10.10.10	UniProtKB/TrEMBL
InterPro	H1/H5	UniProtKB/TrEMBL
	Histone_H1/H5_H15	UniProtKB/TrEMBL
	WH-like_DNA-bd_sf	UniProtKB/TrEMBL
	WH_DNA-bd_sf	UniProtKB/TrEMBL
KEGG Report	csab:103222006	UniProtKB/TrEMBL
NCBI Gene	H1-3	ENTREZGENE
PANTHER	HISTONE H1	UniProtKB/TrEMBL
	HISTONE H1.3	UniProtKB/TrEMBL
Pfam	Linker_histone	UniProtKB/TrEMBL
PRINTS	HISTONEH5	UniProtKB/TrEMBL
PROSITE	H15	UniProtKB/TrEMBL
SMART	H15	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46785	UniProtKB/TrEMBL
UniProt	A0A0D9SCL1	ENTREZGENE, 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)

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