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Gene: HMCES (5-hydroxymethylcytosine binding, ES cell specific) Chlorocebus sabaeus

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Symbol:

HMCES

Name:

5-hydroxymethylcytosine binding, ES cell specific

RGD ID:

18768765

Description:

ENCODES a protein that exhibits DNA-(apurinic or apyrimidinic site) endonuclease activity (ortholog); INVOLVED IN protein-DNA covalent cross-linking repair (ortholog); ASSOCIATED WITH alkaptonuria (ortholog); immunodeficiency 21 (ortholog); Primary Lymphedema with Myelodysplasia (ortholog); FOUND IN chromosome (inferred); replication fork (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

5-hydroxymethylcytosine (hmC) binding, ES cell-specific; abasic site processing protein HMCES; embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein

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	22	51,759,776 - 51,785,902 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	22	51,759,715 - 51,785,987 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666041	114,614,325 - 114,643,816 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

alkaptonuria (ISO)

immunodeficiency 21 (ISO)

Primary Lymphedema with Myelodysplasia (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

DNA damage response (IEA)

DNA repair (IEA)

double-strand break repair via alternative nonhomologous end joining (IEA)

interstrand cross-link repair (IEA)

positive regulation of isotype switching (IEA)

protein-DNA covalent cross-linking repair (IEA,ISO)

proteolysis (IEA)

somatic hypermutation of immunoglobulin genes (IEA)

Cellular Component

chromosome (IEA)

replication fork (IEA)

Molecular Function

DNA binding (IEA)

DNA-(abasic site) binding (IEA)

DNA-(apurinic or apyrimidinic site) endonuclease activity (ISO)

hydrolase activity (IEA)

lyase activity (IEA)

peptidase activity (IEA)

protein binding (ISO)

protein-DNA covalent cross-linking activity (IEA)

single-stranded DNA binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

HMCES
(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	22	51,759,776 - 51,785,902 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	22	51,759,715 - 51,785,987 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666041	114,614,325 - 114,643,816 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

HMCES
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	3	129,278,832 - 129,306,186 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	129,278,828 - 129,306,186 (+)	Ensembl			hg38	GRCh38
GRCh37	3	128,997,675 - 129,025,029 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	130,480,374 - 130,506,826 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Celera	3	127,428,466 - 127,455,235 (+)	NCBI		Celera
Cytogenetic Map	3	q21.3	NCBI
HuRef	3	126,382,730 - 126,409,091 (+)	NCBI		HuRef
CHM1_1	3	128,960,920 - 128,987,406 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	3	132,023,631 - 132,050,984 (+)	NCBI		T2T-CHM13v2.0

Hmces
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	87,890,889 - 87,913,603 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	87,890,917 - 87,913,611 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	6	87,913,907 - 87,936,619 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	87,913,935 - 87,936,629 (+)	Ensembl			mm10	GRCm38
MGSCv37	6	87,863,970 - 87,886,608 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	6	87,879,617 - 87,902,255 (+)	NCBI		MGSCv36	mm8
Celera	6	89,851,062 - 89,873,700 (+)	NCBI		Celera
Cytogenetic Map	6	D1	NCBI
cM Map	6	39.13	NCBI

Hmces
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	121,950,129 - 121,972,937 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	121,950,840 - 121,972,891 (+)	Ensembl				GRCr8
mRatBN7.2	4	120,392,812 - 120,415,616 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	120,366,542 - 120,415,616 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	125,866,062 - 125,888,161 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	121,640,840 - 121,662,940 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	120,265,087 - 120,287,187 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	119,841,088 - 119,864,115 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	119,815,139 - 119,864,114 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	185,088,893 - 185,111,627 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	122,136,275 - 122,154,853 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	109,352,960 - 109,375,056 (+)	NCBI		Celera
Cytogenetic Map	4	q34	NCBI

Hmces
(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_004955429	13,616,647 - 13,661,389 (+)	Ensembl
ChiLan1.0	NW_004955429	13,616,647 - 13,638,657 (+)	NCBI	ChiLan1.0	ChiLan1.0

HMCES
(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	2	127,214,579 - 127,241,990 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	3	127,219,303 - 127,246,714 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	3	126,339,758 - 126,367,166 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	3	133,694,676 - 133,721,519 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	3	133,694,676 - 133,721,519 (+)	Ensembl			panPan2	panpan1.1

HMCES
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	20	2,808,687 - 2,831,123 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	20	2,808,689 - 2,830,462 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	20	2,845,601 - 2,868,050 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	20	2,829,271 - 2,851,755 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	20	2,822,650 - 2,851,729 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	20	2,549,176 - 2,571,634 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	20	2,875,509 - 2,894,638 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	20	2,836,575 - 2,859,069 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Hmces
(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_024404942	20,219,474 - 20,231,141 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936798	261,661 - 273,011 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936798	261,566 - 284,480 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HMCES
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	71,732,277 - 71,753,486 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	13	71,732,311 - 71,752,296 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	79,390,572 - 79,408,184 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

Hmces
(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_004624872	344,262 - 352,936 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624872	344,249 - 353,577 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Variants

Variants in HMCES
516 total Variants

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.

ectoderm	endocrine system	hemolymphoid system	mesenchyme	mesoderm	nervous system	reproductive system
76	36	20	36	36	60	20

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_007985398	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_007985399	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_038003484	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JBLKOC010000022	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSCSAT00000007048 ⟹ ENSCSAP00000005236

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	22	51,759,715 - 51,785,987 (-)	Ensembl

RefSeq Acc Id:

XM_007985398 ⟹ XP_007983589

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	22	51,759,776 - 51,785,902 (-)	NCBI
Vero_WHO_p1.0	NW_023666041	114,614,325 - 114,643,816 (+)	NCBI

Sequence:

show sequence

GTGACGCGAGCTGAGGGAGGTGAAGCGTGCTGCCGGGGCGAGGTTGCGAGGGACGGTGTTGAAG
AATGTGTGGGCGAACATCCTGTCACTTACCTAGAGATGTTCTCACGAGAGCTTGCGCCTACCAG
GATCGGCGGGGCCAGCAGCGGCTCCCGGAATGGAGGGACCCTGATAAGTACTGCCCCTCTTACA
ACAAGAGTCCTCAGTCCAACAGCCCAGTGCTTCTGTCTCGACTGCACTTTGAGAAGGATGCAGA
CTCATCTGAGCGTATCATTGCTCCCATGCGCTGGGGCTTGGTGCCTTCTTGGTTCAAAGAAAGT
GATCCTTCCAAGCTGCAGTTCAATACTACCAACTGTCGTAGTGATACCATAATGGAGAAACGGT
CATTTAAGGTGCCTCTGGGAAAGGGAAGACGCTGTGTCGTTTTAGCAGATGGATTCTATGAGTG
GCAGCGATGTCAAGGAACAAACCAGAGGCAGCCATACTTCATCTATTTTCCTCAAATCAAGACA
GAGAAGTCAGGTAGCACTGGTGCTGCAGATAGTCCTGAGAACTGGGAGAAAGTCTGGGACAACT
GGAGGCTGCTGACAATGGCTGGGATCTTTGACTGCTGGGAGCCCCCAGAGGGAGGAGATGTCCT
GTATTCCTATACTATCATCACAGTGGATTCTTGCAAAGGCTTAAGTGACATCCACCACAGGATG
CCTGCCATATTAGATGGAGAGGAGGCAGTTTCTAAATGGCTTGACTTTGGTGAAGTCTCAACTC
AGGAAGCTCTGAAATTAATCCACTCGACAGAGAACATCACCTTCCATGCAGTCTCTTCTGTGGT
GAACAACTCGCGAAACAATACTCCTGAGTGTCTGGCTCCTGTCGACTTGGTGGTCAAAAAGGAG
CTCAAGGCAAGTGGCAGTAGCCAGAGGATGTTGCAGTGGCTGGCCCCAAAGTCACCCAAAAAGG
AAGACTCAAAAACACCTCAAAAGGAAGAGTCAGATGTTCCCCAGTGGTCCAGTCAGTTCCTGCA
GAAGAGTTCACTCCCCACCAAGAGAGGCACTGCAGGACTCCTAGAGCAATGGCTGAAGCGAGAG
AAGGAAGAGGAACCTGCGGCCAAGCGTCCTTACAGCCAGTGACACAGGACTTTCAGAGACCAAG
GCCAGGGTCTGCCTCACTGCTGTTCTGATAATAGGTTCTTACATTGTATGTGTGTGTGTTTGCT
TTGGGAGGAGGTAGCACTGTGTTGACAGTTGTGGGCTCATGGGGAAGTAGCCTTTTTGGCCATG
AGTAGGAGCCCCTAGTGGGGCTGGTGGACAGCTTTGGAAGAGGTGTCCTGTTGCTGTCACCAGC
CATGTGGGCCCCATAGGGGCACTGTGCCTGCTGCCCTTTTCCTGGCAGGGCTGGTGGAGTCTTC
CCTCAAAGCATGCTTTACCCAGTTGGGAAGTCTCTGCCCTGATCTGGTACTCCTTGTAGTAAGC
TATTTTCTGCTCAGCTACTGGGCTCTTTCAGTTTTTTAGAATAAGTTCTTAAAATGTATTTTTT
TCCTGAATAAATTATGTTTGGTAAACTTCTGCCTACATTTTGGAAAATGATGCTGGTGGGGAAA
GTTCTGGATCTTACTTGTTTTTCTTCTAGAATCAGTCCTCAGGAATGAGTTTTGTCACAAACGG
GGCATGGGGGCTTTCAGAGGAAATAACTACAAGTCTTGGTGGTGGGCTCCTTATTATGTTTCTT
TTTATTTCAGTCTTGATACTTGTAAGTTGTCTGAATCCTTTAGCTTCAAACCAGCCTGAGTTGA
GTGCTTGACACAGCAGAACCTGTCCTGACCACAGGTGGGAAGGAAAGGACCAGTTTCTAGCCGT
GTCGGGCCAGTCCTCTTTTAAGCATCTAGAAGGGAGGCATTCACAAAAGCTGCCCCAACAGCTT
TCGAAATGACCAGGAGGACTGGGCGGCGCCGAGCCCAGAACGCTCCTGACGCAGCCTTGGCTGC
GTTGGCTGCGACCGGACCGATTGCTACTGGTGCGGGGGTGGTGCAGGCCCCAGTCTGTATGCAA
ATCAGGGATCAGAAGATCGGAATTTCCACCAATCAGCGGGAAGCCTCGGCCTCGTAACTGTTAA
TGGGAGACAGCAGCGCCACGCCACAGGCTTTTCCGCTGGAAGGGTGGGGGGCCAGGTGGGGCTC
TCGCCCCCGACCCTTCTCCGAGGCCTGCCCTCCTCGCCTTTTCTCTAAATTCCTCTTTTGAGTG
CCCTCCCTTCCGGTTGAGAGGTGGGGATTGGCCCGTAGTTACACACTCAGTCACCCCGCACTGT
GAAGACCGGGCCTCCCTTGTGAACTGATTTGCGTGGGATTTGGTGGTTTTATTAAGAGATTTAA
AAAATTTAGATGACTTACTAGTATGACTCTTTTGTCGTATTTGCTTCCAGTTTAATAAATGACA
AAAATGAAA

hide sequence

RefSeq Acc Id:

XM_038003484 ⟹ XP_037859412

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
Vero_WHO_p1.0	NW_023666041	114,614,325 - 114,643,816 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_007983589	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000005236.1

RefSeq Acc Id:	XP_007983589 ⟸ XM_007985398
- Peptide Label:	isoform X2
- UniProtKB:	A0A0D9R9E7 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSCSAP00000005236 ⟸ ENSCSAT00000007048

RefSeq Acc Id:	XP_037859412 ⟸ XM_038003484
- Peptide Label:	isoform X1

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000008979	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000007048.1	UniProtKB/TrEMBL
Gene3D-CATH	3.90.1680.10	UniProtKB/TrEMBL
InterPro	SRAP	UniProtKB/TrEMBL
	SRAP-like	UniProtKB/TrEMBL
KEGG Report	csab:103228077	UniProtKB/TrEMBL
NCBI Gene	HMCES	ENTREZGENE
PANTHER	ABASIC SITE PROCESSING PROTEIN HMCES	UniProtKB/TrEMBL
	PTHR13604	UniProtKB/TrEMBL
Pfam	SRAP	UniProtKB/TrEMBL
Superfamily-SCOP	SSF143081	UniProtKB/TrEMBL
UniProt	A0A0D9R9E7	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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