Tdp1 (tyrosyl-DNA phosphodiesterase 1)

Gene: Tdp1 (tyrosyl-DNA phosphodiesterase 1) Ictidomys tridecemlineatus

Analyze

Symbol:

Tdp1

Name:

tyrosyl-DNA phosphodiesterase 1

RGD ID:

12645564

Description:

ENCODES a protein that exhibits 3'-tyrosyl-DNA phosphodiesterase activity (inferred); double-stranded DNA binding (inferred); nuclease activity (inferred); INVOLVED IN DNA repair (ortholog); single strand break repair (ortholog); ASSOCIATED WITH achondrogenesis type IA (ortholog); autosomal recessive cerebellar ataxia (ortholog); genetic disease (ortholog); FOUND IN cytoplasm (ortholog)

Type:

protein-coding

RefSeq Status:

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_024408640	14,757,696 - 14,831,981 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936488	17,236,703 - 17,311,310 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936488	17,237,002 - 17,311,325 (+)	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

achondrogenesis type IA (ISO)

autosomal recessive cerebellar ataxia (ISO)

genetic disease (ISO)

myoepithelioma (ISO)

spinocerebellar ataxia with axonal neuropathy 1 (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

DNA repair (IEA,ISO)

double-strand break repair (IEA)

single strand break repair (IEA,ISO)

Cellular Component

cytoplasm (IEA,ISO)

intracellular membrane-bounded organelle (IEA)

nucleoplasm (IEA)

nucleus (IEA)

plasma membrane (IEA)

Molecular Function

3'-tyrosyl-DNA phosphodiesterase activity (IEA)

double-stranded DNA binding (IEA)

nuclease activity (IEA)

phosphoric diester hydrolase activity (IEA)

protein binding (ISO)

single-stranded DNA binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Tdp1
(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_024408640	14,757,696 - 14,831,981 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936488	17,236,703 - 17,311,310 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936488	17,237,002 - 17,311,325 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TDP1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	14	89,954,968 - 90,044,764 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	14	89,954,939 - 90,044,764 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	14	90,422,271 - 90,511,108 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	89,491,999 - 89,580,861 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	14	89,491,998 - 89,580,859	NCBI
Celera	14	70,469,447 - 70,558,298 (+)	NCBI		Celera
Cytogenetic Map	14	q32.11	NCBI
HuRef	14	70,596,174 - 70,685,067 (+)	NCBI		HuRef
CHM1_1	14	90,360,149 - 90,448,932 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	14	84,179,088 - 84,268,965 (+)	NCBI		T2T-CHM13v2.0

Tdp1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	99,850,767 - 99,921,482 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	99,850,776 - 99,921,478 (+)	Ensembl		GRCm39 Ensembl
GRCm38	12	99,884,515 - 99,955,223 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	99,884,517 - 99,955,219 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	101,122,725 - 101,193,429 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	12	100,285,568 - 100,338,412 (+)	NCBI		MGSCv36	mm8
Celera	12	101,107,017 - 101,181,494 (+)	NCBI		Celera
Cytogenetic Map	12	E	NCBI

Tdp1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	124,892,821 - 124,960,646 (+)	NCBI		GRCr8
mRatBN7.2	6	119,163,192 - 119,231,029 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	119,163,166 - 119,231,021 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	119,314,236 - 119,388,547 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	119,611,041 - 119,685,353 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	118,945,900 - 119,020,218 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	123,895,860 - 123,963,688 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	123,897,956 - 123,963,675 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	133,109,211 - 133,187,083 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	124,095,259 - 124,162,815 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	124,105,017 - 124,166,344 (+)	NCBI
Celera	6	116,696,845 - 116,764,588 (+)	NCBI		Celera
Cytogenetic Map	6	q32	NCBI

Tdp1
(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_004955438	12,421,005 - 12,511,493 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955438	12,421,790 - 12,510,243 (+)	NCBI	ChiLan1.0	ChiLan1.0

TDP1
(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	15	91,099,597 - 91,189,302 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	14	90,316,103 - 90,408,984 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	14	70,574,066 - 70,662,562 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	14	89,926,462 - 90,014,802 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	14	89,926,462 - 90,014,802 (+)	Ensembl	panpan1.1		panPan2

TDP1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	61,023,564 - 61,107,599 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	8	61,024,084 - 61,107,506 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	60,602,950 - 60,687,315 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	8	61,295,027 - 61,379,934 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	8	61,295,370 - 61,379,841 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	8	60,976,795 - 61,061,437 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	8	61,025,579 - 61,109,935 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	8	61,353,607 - 61,438,500 (+)	NCBI		UU_Cfam_GSD_1.0

TDP1
(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	111,767,089 - 111,853,249 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	111,767,094 - 111,853,262 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	118,331,680 - 118,417,900 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TDP1
(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	24	67,672,178 - 67,762,340 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666053	54,975,611 - 55,064,238 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Tdp1
(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_004624734	12,331,710 - 12,414,784 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624734	12,319,499 - 12,414,815 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005321313	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040274199	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005729003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010003700	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSTOT00000004836 ⟹ ENSSTOP00000004341

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936488	17,236,703 - 17,311,310 (+)	Ensembl

RefSeq Acc Id:

XM_005321313 ⟹ XP_005321370

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024408640	14,757,696 - 14,831,981 (-)	NCBI
SpeTri2.0	NW_004936488	17,237,002 - 17,311,325 (+)	NCBI

Sequence:

show sequence

CATGTCTCAGGAAGGCAGTTACGGGAGGTGGACCATATCTAGTAGCGATGAAAGTGAGGATGAG
AAGCCCAAACTGGACAAGCCATCAACATCCTCTCTCTCCCATGCTGGGCAGGGAACAGCCAGTG
AGCCACGGTTCAACTGTTCCGAAGCTCGAAAAGCTGCTCACAGGAGGCAGACATCACCTGTGCA
ATTCAGCAGTGCAGATTTGACTCCACCTCCCAAAAAGCAGAAAAGTGGTTCCCAAGAAGAGCTA
GGCTGGTGTCTCTCCAGCAGTGATGATGAACTGCAACCAGAAACTCAGAAGAAGCAGGCGGAGA
ATGTGGAGGTCAAAGAGGAAAAAGACCTCTCCTCTCCCAAAGATGGTGCTGCCCAGAGAACTGG
AAACCATGGCCTTCCTGCCAGCCACAGGCACAAAAGAGAGGAAGACGAGTATGAGACCTCAGGG
GAAGGCCAAGACATTTGGGACATGCTAGACAAAGGGAACCCCTTCCAGTTCTATCTCACTAGAG
TCTCAGGAATTAAGCCCAAGTACAACTGCAAAGCCCTCCACATCAAGGATATTTTGTCTCCTCT
ATTTGGGACACTTGTTTCTTCAGCTCAGTTCAACTACTGTTTTGATGTAGTCTGGCTCATAAAG
CAGTATCCGCCAGAGTTCAGGAAGAAGCCGATCCTGCTTGTGCATGGTGATAAACGGGAAGCCA
AGGCTCACCTACATGCCCAAGCAAAACCTTATGAGAACGTTTCCCTCTGCCAGGCAAAGTTGGA
TATTGCATTTGGAACACACCACACGAAGATGATGCTACTGCTGTACGAAGAAGGCCTCCGGGTT
GTCATACACACCTCCAACCTCATCCATGAAGACTGGCACCAGAAAACCCAAGGAATATGGTTGA
GCCCCCTATACCCACGAATTGGCCAGCAAACCCACAGATCTGGAGAATCAACAACGCATTTTAA
AGCTGATCTCATCAGTTATTTGAAGGCTTACAATGCCCCTCCTCTTCAGGAGTGGATTGACACC
ATCCAGGAGCACGATCTCTCTGAAACAAATGTTTACCTTATTGGTTCAACCCCCGGACGCTTTC
AAGGAAGTCAGAAGGATAATTGGGGACATTTTAGGCTTAGGAAGCTTCTGAGAGAACACACCTC
GTCAATCCCAAAAGCCGAGTGCTGGCCTATAGTGGGTCAGTTTTCCAGCATTGGCTCACTGGGG
GCTGATGAATCCAAATGGCTGTGTTCTGAGTTTAAAGAGAGCTTGCTGGGCCCCGGGCAGGACA
GTAAAATTCCAGGAAAAAGTACCATTCCTCTTCATTTGATCTATCCTTCTGTGGAAAATGTTCG
GACCAGCTTAGAAGGATACCCTGCTGGAGGTTCTCTTCCCTATAGCATCCAGACAGCTGAAAAA
CAGAATTGGCTACATTCCTACTTCCACACGTGGTCAGCCGACACATCTGGCCGCAGCAATGCCA
TGCCTCATATTAAGACATACATGAGACCCTCTCCAGACTTCAGTAGAATTGCTTGGTTCCTTGT
CACAAGCGCCAACCTGTCCAAAGCCGCTTGGGGAGCACTGGAGAAGAACGGCGCCCAGCTGATG
ATCCGCTCCTACGAGCTTGGGGTGCTCTTCCTCCCGTCAGCATTTGGCCTGGACAGCTTCAAAG
TGAAACAGAAATTCTTCTCTGGCAGCCGGGAGGCAACAGACTTTTTTCCAGTGCCCTATGATCT
GCCCCCAGAACCATACGGAAGTAAAGATCGGCCATGGATTTGGAACATTCCTTATATCAAAGCG
CCAGATACACACGGGAACATGTGGGTGCCCTCCTGAGAATCTTAAAGCACTGTGAAATTGAGCA
TAAGATGTTGAGCCCCAAACCTTGGATATTCTTGTGAACACTGGGTGTTCATTTCCCTTAAAAT
CTGACTTGCATCCCTGCAAAACTCATGAAGGTTGCTCTTGTGAACTTGGATGTTGGTTATACTT
TTAATGTTTATTGTCAGCATTCTCACTTTAAAAAAAAAAAAGTGTTATTTTCTTATTCACTTTT
ATATGTTTTGGAAAGAAAGCTATTAAACTTCACATGTTAAAAATATGTATCTATGCCGATATGA
AATTACCCCCCTACTGAAGAGGACTCAGATCTCA

hide sequence

RefSeq Acc Id:

XM_040274199 ⟹ XP_040130133

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024408640	14,757,942 - 14,831,981 (-)	NCBI

RefSeq Acc Id:

XR_005729003

Type:

NON-CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024408640	14,757,696 - 14,831,981 (-)	NCBI

Protein Sequences


Protein RefSeqs	XP_005321370	(Get FASTA)	NCBI Sequence Viewer
	XP_040130133	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000004341.3
GenBank Protein	KAG3260534	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	XP_005321370 ⟸ XM_005321313
- Peptide Label:	isoform X1
- UniProtKB:	I3M4Y6 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSQEGSYGRWTISSSDESEDEKPKLDKPSTSSLSHAGQGTASEPRFNCSEARKAAHRRQTSPVQ FSSADLTPPPKKQKSGSQEELGWCLSSSDDELQPETQKKQAENVEVKEEKDLSSPKDGAAQRTG NHGLPASHRHKREEDEYETSGEGQDIWDMLDKGNPFQFYLTRVSGIKPKYNCKALHIKDILSPL FGTLVSSAQFNYCFDVVWLIKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENVSLCQAKLD IAFGTHHTKMMLLLYEEGLRVVIHTSNLIHEDWHQKTQGIWLSPLYPRIGQQTHRSGESTTHFK ADLISYLKAYNAPPLQEWIDTIQEHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLRKLLREHTS SIPKAECWPIVGQFSSIGSLGADESKWLCSEFKESLLGPGQDSKIPGKSTIPLHLIYPSVENVR TSLEGYPAGGSLPYSIQTAEKQNWLHSYFHTWSADTSGRSNAMPHIKTYMRPSPDFSRIAWFLV TSANLSKAAWGALEKNGAQLMIRSYELGVLFLPSAFGLDSFKVKQKFFSGSREATDFFPVPYDL PPEPYGSKDRPWIWNIPYIKAPDTHGNMWVPS hide sequence

RefSeq Acc Id:	XP_040130133 ⟸ XM_040274199
- Peptide Label:	isoform X2
- UniProtKB:	I3M4Y6 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSSTOP00000004341 ⟸ ENSSTOT00000004836

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000004829	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000004836.3	UniProtKB/TrEMBL
Gene3D-CATH	Endonuclease Chain A	UniProtKB/TrEMBL
InterPro	Tdp1	UniProtKB/TrEMBL
NCBI Gene	Tdp1	ENTREZGENE
PANTHER	PTHR12415	UniProtKB/TrEMBL
	TYROSYL-DNA PHOSPHODIESTERASE 1	UniProtKB/TrEMBL
Pfam	Tyr-DNA_phospho	UniProtKB/TrEMBL
Superfamily-SCOP	Phospholipase D/nuclease	UniProtKB/TrEMBL
UniProt	I3M4Y6	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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Imported Disease Annotations - ClinVar

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