Tdp2 (tyrosyl-DNA phosphodiesterase 2)

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Gene: Tdp2 (tyrosyl-DNA phosphodiesterase 2) Chinchilla lanigera

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Symbol:

Tdp2

Name:

tyrosyl-DNA phosphodiesterase 2

RGD ID:

8875499

Description:

ENCODES a protein that exhibits 5'-tyrosyl-DNA phosphodiesterase activity (ortholog); magnesium ion binding (ortholog); manganese ion binding (ortholog); INVOLVED IN double-strand break repair (ortholog); neuron development (ortholog); ASSOCIATED WITH autosomal recessive spinocerebellar ataxia 23 (ortholog); cerebellar ataxia (ortholog); genetic disease (ortholog); FOUND IN aggresome (ortholog); cytoplasm (ortholog); nuclear body (ortholog)

Type:

protein-coding

RefSeq Status:

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955483	2,375,313 - 2,388,892 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955483	2,375,213 - 2,385,354 (+)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autosomal recessive spinocerebellar ataxia 23 (ISO)

cerebellar ataxia (ISO)

genetic disease (ISO)

Spinocerebellar Ataxias (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

double-strand break repair (ISO)

neuron development (ISO)

Cellular Component

aggresome (ISO)

cytoplasm (ISO)

nuclear body (ISO)

nucleoplasm (ISO)

nucleus (ISO)

PML body (ISO)

Molecular Function

5'-tyrosyl-DNA phosphodiesterase activity (ISO)

magnesium ion binding (ISO)

manganese ion binding (ISO)

protein binding (ISO)

single-stranded DNA binding (ISO)

tyrosyl-RNA phosphodiesterase activity (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Tdp2
(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_004955483	2,375,313 - 2,388,892 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955483	2,375,213 - 2,385,354 (+)	NCBI	ChiLan1.0	ChiLan1.0

TDP2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	24,649,979 - 24,666,899 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	24,649,979 - 24,666,930 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	24,650,207 - 24,667,127 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	24,758,184 - 24,775,094 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	6	24,758,184 - 24,775,094	NCBI
Celera	6	25,883,542 - 25,900,457 (-)	NCBI		Celera
Cytogenetic Map	6	p22.3	NCBI
HuRef	6	24,599,621 - 24,616,537 (-)	NCBI		HuRef
CHM1_1	6	24,654,343 - 24,671,259 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	24,520,363 - 24,537,292 (-)	NCBI		T2T-CHM13v2.0

Tdp2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	25,015,642 - 25,026,136 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	13	25,015,662 - 25,026,136 (+)	Ensembl		GRCm39 Ensembl
GRCm38	13	24,831,659 - 24,842,153 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	24,831,679 - 24,842,153 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	13	24,923,528 - 24,934,022 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	13	24,839,150 - 24,849,611 (+)	NCBI		MGSCv36	mm8
Celera	13	25,062,324 - 25,072,818 (+)	NCBI		Celera
Cytogenetic Map	13	A3.1	NCBI
cM Map	13	10.7	NCBI

Tdp2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	17	40,656,969 - 40,668,362 (-)	NCBI		GRCr8
mRatBN7.2	17	40,228,943 - 40,240,337 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	17	40,228,947 - 40,240,313 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	17	40,297,128 - 40,308,451 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	17	41,901,173 - 41,912,496 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	17	40,184,268 - 40,195,590 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	17	42,229,667 - 42,241,025 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	17	42,229,642 - 42,241,066 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	17	44,097,466 - 44,108,824 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	47,290,530 - 47,301,849 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	17	39,866,248 - 39,877,568 (-)	NCBI		Celera
Cytogenetic Map	17	p11	NCBI

TDP2
(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	39,300,990 - 39,318,562 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	35,300,448 - 35,318,023 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	24,487,551 - 24,505,268 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	24,819,494 - 24,837,189 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	24,819,494 - 24,837,189 (-)	Ensembl	panpan1.1		panPan2

TDP2
(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	22,693,203 - 22,707,054 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	35	22,693,110 - 22,707,008 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	35	22,660,843 - 22,674,624 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	35	22,815,655 - 22,829,433 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	35	22,814,198 - 22,829,404 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	35	22,621,127 - 22,634,899 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	35	22,668,709 - 22,682,476 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	35	24,105,036 - 24,118,785 (-)	NCBI		UU_Cfam_GSD_1.0

Tdp2
(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_024411772	475 - 1,113 (-)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004948563	494 - 1,113 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TDP2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	19,489,384 - 19,502,520 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	19,489,381 - 19,502,437 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	20,642,148 - 20,655,198 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TDP2
(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	47,582,857 - 47,599,871 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	47,583,014 - 47,600,628 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666044	24,580,645 - 24,597,659 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Tdp2
(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_004624756	2,363,718 - 2,375,152 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624756	2,363,400 - 2,374,839 (+)	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_005403367	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_005403368	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01057675	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDF01254328	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSCLAT00000002938 ⟹ ENSCLAP00000002881

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955483	2,375,313 - 2,388,892 (+)	Ensembl

RefSeq Acc Id:

XM_005403367 ⟹ XP_005403424

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955483	2,375,213 - 2,385,354 (+)	NCBI

Sequence:

show sequence

CGCCGGGTGGTAGATGCGGGTGCACCAGGGCGCCAGGCGCCTGCGCAGAACTGGGCAGCGGCTG
CGCCTTTAAAGTGGGCGTTGTAAACACGGCGAGGTGATGGAGCTCGGGAGCAGTGAGGAGGAGG
CGCGGGACGAGAGCCAGCCCGAGGCGAAGAGGCGGCGGTTGCTGTGCGTGCAGTTCTCCTCGGT
GGCGAGCTGCGACGCCGCGGTGGCGCAGGGGTACCTGGCCGAGAACAACTGGGAGATGGAAAGA
GCGCTGAACTCCTACTTCGAGCCCGCCGCGGAGGGCAGTGCGGTGGGAAGCCGGGCCGGGCTGC
CAGCGGAGCCCGGGCGTTGTGTTGACCTAACCAATGAAGAAACAACTGATTCCACTAGTTCTAA
AGTCTGCTCATCTGAAAACATTCAGCAAGAAGATGGCAGTATGTTCTCTTTCATCACGTGGAAC
ATTGATGGATTGGATCTAAACAGTCTCCAAGAGAGGGCTCGAGGGGTGTGTTCCTATTTAGCTC
TGTACAACCCGGATGTCGTATTTCTACAGGAAGTTATTCCACCCTATTTTAGCTATCTGAAGAA
GAGAGCAAGTAGTTATGAGATTATTACAGGTCACGAAGAAGGCTATTTCACAGCTATAATGTTG
AAGAAGTCGAGAGTGAAATTAAAAAGCCAAGAGATCATTCCTTTTCCAAGTACCAAGATGATGA
GGAACCTTTTGTGTGTGCATGTGAGTTTGTCTGGAAATGAACTTTGCCTTATGACTTCCCATTT
GGAGAGCACCAGAGGGCACGCCAGCGAACGAATGAATCAGTTAAAACTGGTGTTAAAGAAAATG
CAAGAGGCTCCAGAGTCAGCTACAGTTATATTTGCAGGAGATACCAATTTAAGGGATCAAGAAG
TGACTAAATGTGGTGGTTTACCCAGCAACATTTTGGATGTCTGGGAGTTTTTGGGCAAACCTAA
GCATTGCCAGTATACATGGGACACACAGATGAACTCTAATCTTGGAATACCTGCTACTTGTAAG
CTTCGTTTTGATCGAATATTTTTCAGAGCAGCAGCAGAAGAGGGCCACATTATTCCTCGAAGTT
TGGACCTGCTTGGGTTGGAGAAACTGGACTGTGGCAGATTTCCTAGTGATCACTGGGGTCTGCT
GTGTAATTTAGATGTCATATTGTGAAATACTTTACAAATATGAGTCTTAAGTGTTTTATTTTGT
GCTGGATTTTTGCAGATGTAATTTCTTCCTATCTGGAAAGGTCAATTTAATATGGAGAAATTAA
TACTGTAAAGTGGATCATTGCTACAGGAAAACACAGTTACAATTTTGAATTATGGATTATGTCC
TCAGAATTAGAATCAGCCAGGTGTGGTGGTGCACACCTGTAATCTCAGCACCTGAGAGACTGAG
TCAGGATTGTTGTGAGTTTGAGG

hide sequence

RefSeq Acc Id:

XM_005403368 ⟹ XP_005403425

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955483	2,375,213 - 2,385,354 (+)	NCBI

Sequence:

show sequence

CGCCGGGTGGTAGATGCGGGTGCACCAGGGCGCCAGGCGCCTGCGCAGAACTGGGCAGCGGCTG
CGCCTTTAAAGTGGGCGTTGTAAACACGGCGAGGTGATGGAGCTCGGGAGCAGTGAGGAGGAGG
CGCGGGACGAGAGCCAGCCCGAGGCGAAGAGGCGGCGGTTGCTGTGCGTGCAGTTCTCCTCGGT
GGCGAGCTGCGACGCCGCGGTGGCGCAGGGGTACCTGGCCGAGAACAACTGGGAGATGGAAAGA
GCGCTGAACTCCTACTTCGAGCCCGCCGCGGAGGGCAGTGCGGTGGGAAGCCGGGCCGGGCTGC
CAGCGGAGCCCGGGCGTTGTGTTGACCTAACCAATGAAGAAACAACTGATTCCACTAGTTCTAA
AGTCTGCTCATCTGAAAACATTCAGCAAGAAGATGGCAGTATGTTCTCTTTCATCACGTGGAAC
ATTGATGGATTGGATCTAAACAGTCTCCAAGAGAGGGCTCGAGGGGTGTGTTCCTATTTAGCTC
TGTACAACCCGGATGTCGTATTTCTACAGGAAGTTATTCCACCCTATTTTAGCTATCTGAAGAA
GAGAGCAAGTAGTTATGAGATTATTACAGGTCACGAAGAAGGCTATTTCACAGCTATAATGTTG
AAGAAGTCGAGAGTGAAATTAAAAAGCCAAGAGATCATTCCTTTTCCAAGTACCAAGATGATGA
GGAACCTTTTGTGTGTGCATGTGACTAAATGTGGTGGTTTACCCAGCAACATTTTGGATGTCTG
GGAGTTTTTGGGCAAACCTAAGCATTGCCAGTATACATGGGACACACAGATGAACTCTAATCTT
GGAATACCTGCTACTTGTAAGCTTCGTTTTGATCGAATATTTTTCAGAGCAGCAGCAGAAGAGG
GCCACATTATTCCTCGAAGTTTGGACCTGCTTGGGTTGGAGAAACTGGACTGTGGCAGATTTCC
TAGTGATCACTGGGGTCTGCTGTGTAATTTAGATGTCATATTGTGAAATACTTTACAAATATGA
GTCTTAAGTGTTTTATTTTGTGCTGGATTTTTGCAGATGTAATTTCTTCCTATCTGGAAAGGTC
AATTTAATATGGAGAAATTAATACTGTAAAGTGGATCATTGCTACAGGAAAACACAGTTACAAT
TTTGAATTATGGATTATGTCCTCAGAATTAGAATCAGCCAGGTGTGGTGGTGCACACCTGTAAT
CTCAGCACCTGAGAGACTGAGTCAGGATTGTTGTGAGTTTGAGG

hide sequence

Protein Sequences


Protein RefSeqs	XP_005403424	(Get FASTA)	NCBI Sequence Viewer
	XP_005403425	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000002881
	ENSCLAP00000002881.1

RefSeq Acc Id:	XP_005403424 ⟸ XM_005403367
- Peptide Label:	isoform X1
- UniProtKB:	A0A8C2UTE1 (UniProtKB/TrEMBL)
- Sequence:	show sequence MELGSSEEEARDESQPEAKRRRLLCVQFSSVASCDAAVAQGYLAENNWEMERALNSYFEPAAEG SAVGSRAGLPAEPGRCVDLTNEETTDSTSSKVCSSENIQQEDGSMFSFITWNIDGLDLNSLQER ARGVCSYLALYNPDVVFLQEVIPPYFSYLKKRASSYEIITGHEEGYFTAIMLKKSRVKLKSQEI IPFPSTKMMRNLLCVHVSLSGNELCLMTSHLESTRGHASERMNQLKLVLKKMQEAPESATVIFA GDTNLRDQEVTKCGGLPSNILDVWEFLGKPKHCQYTWDTQMNSNLGIPATCKLRFDRIFFRAAA EEGHIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLDVIL hide sequence

RefSeq Acc Id:

XP_005403425 ⟸ XM_005403368

- Peptide Label:

isoform X2

- Sequence:

show sequence

MELGSSEEEARDESQPEAKRRRLLCVQFSSVASCDAAVAQGYLAENNWEMERALNSYFEPAAEG
SAVGSRAGLPAEPGRCVDLTNEETTDSTSSKVCSSENIQQEDGSMFSFITWNIDGLDLNSLQER
ARGVCSYLALYNPDVVFLQEVIPPYFSYLKKRASSYEIITGHEEGYFTAIMLKKSRVKLKSQEI
IPFPSTKMMRNLLCVHVTKCGGLPSNILDVWEFLGKPKHCQYTWDTQMNSNLGIPATCKLRFDR
IFFRAAAEEGHIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLDVIL

hide sequence

Ensembl Acc Id:

ENSCLAP00000002881 ⟸ ENSCLAT00000002938

Protein Domains

Endonuclease/exonuclease/phosphatase

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000002072	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000002938	ENTREZGENE
	ENSCLAT00000002938.1	UniProtKB/TrEMBL
Gene3D-CATH	3.60.10.10	UniProtKB/TrEMBL
	DNA helicase RuvA subunit, C-terminal domain	UniProtKB/TrEMBL
InterPro	Endo/exonu/phosph_ase_sf	UniProtKB/TrEMBL
	Endo/exonuclease/phosphatase	UniProtKB/TrEMBL
	TDP2-like	UniProtKB/TrEMBL
	UBA-like_sf	UniProtKB/TrEMBL
NCBI Gene	Tdp2	ENTREZGENE
PANTHER	TRAF AND TNF RECEPTOR-ASSOCIATED PROTEIN	UniProtKB/TrEMBL
	TYROSYL-DNA PHOSPHODIESTERASE 2	UniProtKB/TrEMBL
Pfam	Exo_endo_phos	UniProtKB/TrEMBL
	UBA_4	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46934	UniProtKB/TrEMBL
	SSF56219	UniProtKB/TrEMBL
UniProt	A0A8C2UTE1	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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