Xpa (XPA, DNA damage recognition and repair factor)

Gene: Xpa (XPA, DNA damage recognition and repair factor) Ictidomys tridecemlineatus

Analyze

Symbol:

Xpa

Name:

XPA, DNA damage recognition and repair factor

RGD ID:

12656206

Description:

ENCODES a protein that exhibits damaged DNA binding (inferred); DNA binding (inferred); metal ion binding (inferred); INVOLVED IN DNA repair (ortholog); intrinsic apoptotic signaling pathway in response to DNA damage (ortholog); multicellular organism growth (ortholog); PARTICIPATES IN altered nucleotide excision repair pathway; nucleotide excision repair pathway; ASSOCIATED WITH basal cell carcinoma (ortholog); Cockayne syndrome (ortholog); congenital disorder of glycosylation Ii (ortholog); FOUND IN DNA replication factor A complex (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

DNA repair protein complementing XP-A cells

RGD Orthologs

Alliance Genes

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_024404947	169,920,223 - 169,945,978 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936524	6,465,104 - 6,493,610 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936524	6,467,365 - 6,493,556 (-)	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

basal cell carcinoma (ISO)

Cockayne syndrome (ISO)

congenital disorder of glycosylation Ii (ISO)

congenital disorder of glycosylation type II (ISO)

congenital myasthenic syndrome 14 (ISO)

Generalized Epilepsy (ISO)

genetic disease (ISO)

intellectual disability (ISO)

Intestinal Neoplasms (ISO)

Liver Neoplasms (ISO)

Micronuclei, Chromosome-Defective (ISO)

nephronophthisis (ISO)

ovarian cancer (ISO)

Skin Neoplasms (ISO)

thoracic aortic aneurysm (ISO)

xeroderma pigmentosum (ISO)

xeroderma pigmentosum group A (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

base-excision repair (IEA)

DNA damage response (IEA)

DNA repair (IEA,ISO)

intrinsic apoptotic signaling pathway in response to DNA damage (ISO)

multicellular organism growth (ISO)

nucleotide-excision repair (IEA,ISO)

nucleotide-excision repair involved in interstrand cross-link repair (IEA)

nucleotide-excision repair, DNA damage recognition (IEA)

positive regulation of transcription initiation by RNA polymerase II (ISO)

protein localization to nucleus (IEA)

regulation of autophagy (ISO)

response to auditory stimulus (ISO)

response to oxidative stress (ISO)

response to toxic substance (ISO)

response to UV (ISO)

UV protection (IEA)

UV-damage excision repair (IEA)

Cellular Component

DNA replication factor A complex (IEA,ISO)

intercellular bridge (IEA)

nucleoplasm (IEA)

nucleotide-excision repair factor 1 complex (IEA)

nucleus (IEA)

Molecular Function

damaged DNA binding (IEA)

DNA binding (IEA)

metal ion binding (IEA)

protein binding (ISO)

protein domain specific binding (IEA)

protein homodimerization activity (IEA)

sequence-specific double-stranded DNA binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

altered nucleotide excision repair pathway (ISO)

nucleotide excision repair pathway (ISO)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Xpa
(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_024404947	169,920,223 - 169,945,978 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936524	6,465,104 - 6,493,610 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936524	6,467,365 - 6,493,556 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

XPA
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	97,654,398 - 97,697,340 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	97,674,909 - 97,697,340 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	100,437,191 - 100,459,622 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	99,477,012 - 99,499,512 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	97,516,746 - 97,539,194	NCBI
Celera	9	70,951,417 - 70,973,928 (-)	NCBI		Celera
Cytogenetic Map	9	q22.33	NCBI
HuRef	9	70,038,231 - 70,060,725 (-)	NCBI		HuRef
CHM1_1	9	100,583,626 - 100,606,139 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	9	109,826,339 - 109,869,281 (-)	NCBI		T2T-CHM13v2.0

Xpa
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	46,175,222 - 46,196,317 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	46,155,347 - 46,196,311 (-)	Ensembl		GRCm39 Ensembl
GRCm38	4	46,175,220 - 46,196,344 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	46,155,347 - 46,196,311 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	46,188,094 - 46,209,183 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	4	46,196,339 - 46,217,411 (-)	NCBI		MGSCv36	mm8
Celera	4	46,197,357 - 46,218,441 (-)	NCBI		Celera
Cytogenetic Map	4	B1	NCBI
cM Map	4	24.49	NCBI

Xpa
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	65,227,281 - 65,275,784 (-)	NCBI		GRCr8
mRatBN7.2	5	60,431,673 - 60,475,726 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	60,431,673 - 60,475,726 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	62,404,102 - 62,448,198 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	64,223,605 - 64,267,701 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	64,192,858 - 64,236,954 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	61,749,767 - 61,793,641 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	61,749,767 - 61,792,928 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	66,266,229 - 66,310,103 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	62,706,719 - 62,750,771 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	62,726,371 - 62,750,949 (-)	NCBI
Celera	5	58,992,396 - 59,036,208 (-)	NCBI		Celera
Cytogenetic Map	5	q22	NCBI

Xpa
(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_004955419	27,751,043 - 27,774,917 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955419	27,751,042 - 27,774,917 (+)	NCBI	ChiLan1.0	ChiLan1.0

XPA
(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	11	41,759,709 - 41,823,406 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	9	41,762,094 - 41,825,789 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	68,726,723 - 68,788,049 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	96,866,303 - 96,909,260 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	96,886,795 - 96,909,254 (-)	Ensembl	panpan1.1		panPan2

XPA
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	11	54,976,978 - 54,996,140 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	11	54,976,976 - 54,996,065 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	11	53,406,654 - 53,430,263 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	11	56,085,046 - 56,108,618 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	11	56,088,588 - 56,108,630 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	11	54,581,396 - 54,605,007 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	11	54,611,286 - 54,634,866 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	11	55,307,954 - 55,331,573 (-)	NCBI		UU_Cfam_GSD_1.0

XPA
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	239,532,272 - 239,568,570 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	239,532,331 - 239,568,589 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	267,660,926 - 267,694,917 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

XPA
(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	12	41,711,872 - 41,735,024 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	12	41,711,943 - 41,725,698 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666038	38,764,911 - 38,788,051 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Xpa
(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_004624825	3,137,823 - 3,162,294 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624825	3,138,386 - 3,162,774 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005326308	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSTOT00000002712 ⟹ ENSSTOP00000002427

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936524	6,465,104 - 6,493,610 (-)	Ensembl

RefSeq Acc Id:

XM_005326308 ⟹ XP_005326365

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404947	169,920,223 - 169,945,978 (-)	NCBI
SpeTri2.0	NW_004936524	6,467,365 - 6,493,556 (-)	NCBI

Sequence:

show sequence

CCTTCCTGCGGCACCCTCGGTCGAGGGACATGGAAGTGGTGGCGGCGTCGCAGCCGACCGTGGG
CACTCCTCCGTACGCAATGCGCAAGCGCGGGGCCGGGCCGCTTTCTTCCGAGCTGGACGGAGAT
GGCGGCAGCGGAGAGTGTTTCGCCGGAGCTGGCGGCTTCGGAGCAGCCGGGGGAGCTGCCTGCC
TCGGTGCGGGCGAGCATCGAGCGGAAGCGGCAGCGGGCGCTGATGCTGCGTCAGGCCCGGCTGG
CAGCCCGGCCCTACCCGGCGACGGCGGCTGCGGCCACTGGAGGTGTGGCTAATGTAAAAGCAGC
CCCCAAAATAATTGACACAAAAGGAGGCTTTATTTTAGAAGAGGAAGTAGAAGAAGAACATAAA
ATTGGAAACATTGTTCATCAACCAGGACCTGTTATGGAATTTGATTATGTAATATGTGAAGAAT
GTGGGAAAGAATTTATGGATTCTTATCTTATGAAACACTTTGATTTGGCAACTTGTGATAACTG
CAGAGATGCTGATGAGAAACACAAACTTATTACCAAAACAGAAGCAAAACAAGAATACCTCCTG
AAGGACTGTGATTTAGAAAAAAGAGAACCAGCTCTTAAATTTATTGTGAAGAAGAATCCTCATC
ATTCACAGTGGGGTGATATGAAACTCTACTTAAAATTACAGATTGTGAAGAGGTCCCTTGAAGT
TTGGGGTAGTCAGGAAGCACTAGAAGAAGCAAAGGAAGTGAGACAAGAAAACAGAGAAAAAATG
AAACAAAAGAAGTTTGATAAAAAAGTAAAAGAATTGCGCCGGGCAGTAAGAAGCAGTGTATGGA
AAAGAGAATTGACTGCTCATCAACATGAGTATGGACCAGAAGAAAACTTAGAAGATGACATGTA
CCGCAAGACTTGTACTGTGTGTGGCCATGAACTGACATATGAAAAAATGTGATTTTTTTAGTTT
CACTTGACATTTTTAACAGAAATTTATATTTAAATAAAGGAAATTAGATTGGCTTTATTCAGAA
TTCACCACAATGTAGTCCTTATAAATGACACACTTGCATAAATGCTTCATTTTAAGAGAAAGTT
ACAGTCCAGCTGGTCTGGTCCAGGGCAGCATATCAGAGTAGGAGGTGAATGGTAGAATGGGTTT
AAAGCGGCAGGTCAGATCTGCAAATGGGGGAGCAAGAGGATAAAGCAAATCCTCCAATGGCGCA
GAAAGAAGAGCTTTCAATAAAGGTCAAAGTTGACTGAACAGGGATGGTGGTATACTGTTGTAAG
AGTCTGTCAGGACTTTAAGGACTACTTCTATCTCTAGGACAGTGAGGACAGTGAGGCAGTCCTG
AGGAGCCAAAGCTGGAAGAAGTCCTAGCATCAAGAATAAACAAATTGCAGGATTCTGGTCATGT
TTTCACTAAGGGCTTACTACTCAAATGCTGAATTAAAATGGAAAGCAGCTTCTTTGAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_005326365	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000002427.3
GenBank Protein	KAG3287575	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_005326365 ⟸ XM_005326308

- UniProtKB:

I3M0Y9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAAAESVSPELAASEQPGELPASVRASIERKRQRALMLRQARLAARPYPATAAAATGGVANVKA
APKIIDTKGGFILEEEVEEEHKIGNIVHQPGPVMEFDYVICEECGKEFMDSYLMKHFDLATCDN
CRDADEKHKLITKTEAKQEYLLKDCDLEKREPALKFIVKKNPHHSQWGDMKLYLKLQIVKRSLE
VWGSQEALEEAKEVRQENREKMKQKKFDKKVKELRRAVRSSVWKRELTAHQHEYGPEENLEDDM
YRKTCTVCGHELTYEKM

hide sequence

RefSeq Acc Id:

ENSSTOP00000002427 ⟸ ENSSTOT00000002712

Protein Domains

XPA C-terminal

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000002720	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000002712.3	UniProtKB/TrEMBL
Gene3D-CATH	3.90.530.10	UniProtKB/TrEMBL
InterPro	DNA-bd_dom_put_sf	UniProtKB/TrEMBL
	XPA	UniProtKB/TrEMBL
	XPA_C	UniProtKB/TrEMBL
	XPA_CS	UniProtKB/TrEMBL
	XPA_sf	UniProtKB/TrEMBL
	Znf_XPA_CS	UniProtKB/TrEMBL
NCBI Gene	Xpa	ENTREZGENE
PANTHER	DNA REPAIR PROTEIN COMPLEMENTING XP-A CELLS	UniProtKB/TrEMBL
	PTHR10142	UniProtKB/TrEMBL
Pfam	XPA_C	UniProtKB/TrEMBL
	XPA_N	UniProtKB/TrEMBL
PROSITE	XPA_1	UniProtKB/TrEMBL
	XPA_2	UniProtKB/TrEMBL
Superfamily-SCOP	Glucocorticoid receptor-like (DNA-binding domain)	UniProtKB/TrEMBL
	SSF46955	UniProtKB/TrEMBL
UniProt	I3M0Y9	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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - SMPDB

Send us a Message

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - SMPDB