Aplf (aprataxin and PNKP like factor)

Gene: Aplf (aprataxin and PNKP like factor) Ictidomys tridecemlineatus

Analyze

Symbol:

Aplf

Name:

aprataxin and PNKP like factor

RGD ID:

12709555

Description:

ENCODES a protein that exhibits protein folding chaperone (ortholog); INVOLVED IN double-strand break repair (ortholog); positive regulation of DNA ligation (ortholog); regulation of isotype switching (ortholog); PARTICIPATES IN ADP-ribosylation pathway, mono and poly-ribosylation; histone modification pathway; non-homologous end joining pathway of double-strand break repair; ASSOCIATED WITH genetic disease (ortholog); FOUND IN cytosol (ortholog); nucleus (ortholog); site of DNA damage (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

aprataxin and PNK-like factor

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_024406292	15,609,577 - 15,713,285 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936491	12,857,785 - 12,962,376 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936491	12,857,928 - 12,961,709 (+)	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

genetic disease (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

DNA damage response (IEA)

DNA repair (IEA)

DNA repair-dependent chromatin remodeling (IEA)

double-strand break repair (IEA,ISO)

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

embryo implantation (IEA)

positive regulation of DNA ligation (IEA,ISO)

protein localization to chromatin (IEA)

regulation of epithelial to mesenchymal transition (IEA)

regulation of isotype switching (IEA,ISO)

single strand break repair (IEA)

Cellular Component

cytosol (IEA,ISO)

nucleoplasm (IEA)

nucleus (IEA,ISO)

site of DNA damage (IEA,ISO)

site of double-strand break (IEA,ISO)

Molecular Function

3'-5' exonuclease activity (IEA)

ADP-D-ribose modification-dependent protein binding (IEA)

DNA endonuclease activity (IEA)

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

histone binding (IEA)

histone chaperone activity (IEA)

hydrolase activity (IEA)

nucleotide binding (IEA)

poly-ADP-D-ribose binding (IEA)

protein binding (ISO)

protein folding chaperone (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

ADP-ribosylation pathway, mono and poly-ribosylation (ISO)

histone modification pathway (ISO)

non-homologous end joining pathway of double-strand break repair (ISO)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Aplf
(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_024406292	15,609,577 - 15,713,285 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936491	12,857,785 - 12,962,376 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936491	12,857,928 - 12,961,709 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

APLF
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	68,467,585 - 68,580,162 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	68,467,572 - 68,655,862 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	68,694,717 - 68,807,294 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	68,548,246 - 68,660,798 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	68,606,392 - 68,718,944	NCBI
Celera	2	68,544,671 - 68,657,741 (+)	NCBI		Celera
Cytogenetic Map	2	p13.3	NCBI
HuRef	2	68,431,541 - 68,543,835 (+)	NCBI		HuRef
CHM1_1	2	68,624,013 - 68,736,628 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	68,479,947 - 68,592,502 (+)	NCBI		T2T-CHM13v2.0

Aplf
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	87,605,407 - 87,649,244 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	87,605,406 - 87,649,175 (-)	Ensembl		GRCm39 Ensembl
GRCm38	6	87,628,425 - 87,672,237 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	87,628,424 - 87,672,193 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	87,578,423 - 87,622,162 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	87,594,070 - 87,637,788 (-)	NCBI		MGSCv36	mm8
Celera	6	89,562,818 - 89,606,576 (-)	NCBI		Celera
Cytogenetic Map	6	D1	NCBI
cM Map	6	38.52	NCBI

Aplf
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	121,627,800 - 121,679,980 (-)	NCBI		GRCr8
mRatBN7.2	4	120,070,471 - 120,122,656 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	120,070,471 - 120,122,633 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	125,544,041 - 125,602,785 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	121,318,838 - 121,377,584 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	119,943,068 - 120,001,808 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	119,514,822 - 119,568,764 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	119,514,840 - 119,568,736 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	184,767,521 - 184,809,501 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Rnor_5.0	4	184,816,979 - 184,819,739 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	121,796,926 - 121,849,410 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	4	109,037,717 - 109,083,976 (-)	NCBI		Celera
Cytogenetic Map	4	q34	NCBI

Aplf
(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_004955424	16,336,228 - 16,448,766 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955424	16,338,546 - 16,449,074 (-)	NCBI	ChiLan1.0	ChiLan1.0

APLF
(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	12	57,836,254 - 57,947,492 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	57,838,385 - 57,951,427 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	68,509,314 - 68,629,192 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	69,632,459 - 69,744,611 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	69,632,459 - 69,744,611 (+)	Ensembl	panpan1.1		panPan2

APLF
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	10	67,454,500 - 67,522,659 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	67,454,356 - 67,521,761 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	67,344,455 - 67,413,321 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	68,473,928 - 68,543,022 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	68,473,934 - 68,546,201 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	68,156,771 - 68,224,622 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	68,455,171 - 68,524,808 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	68,750,534 - 68,819,077 (+)	NCBI		UU_Cfam_GSD_1.0

APLF
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	73,752,118 - 73,831,035 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	73,752,115 - 73,831,158 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	77,287,005 - 77,362,138 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

APLF
(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	14	38,539,398 - 38,636,666 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	14	38,540,084 - 38,636,569 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	73,339,984 - 73,456,338 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Aplf
(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_004624762	4,724,813 - 4,847,416 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624762	4,727,834 - 4,847,779 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_021724318	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040271101	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010001352	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSTOT00000014679 ⟹ ENSSTOP00000013149

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936491	12,857,785 - 12,962,376 (+)	Ensembl

RefSeq Acc Id:

XM_021724318 ⟹ XP_021579993

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024406292	15,609,577 - 15,713,278 (-)	NCBI
SpeTri2.0	NW_004936491	12,857,928 - 12,961,709 (+)	NCBI

Sequence:

show sequence

CGATTGCGTCACTCGTTCGGGTGGAGGGCGGGACTCCGGAAGTGGCGCTGGGGCCCCTGCCCCT
CAAGGAGTGAACTCTCCCGAGCTGAGCCTTTGCTCCCCCTTCCCCTCCCCCTCCCCCTCTGTTT
TCCAGGGGCCTGGGCATGCCCCGCGCGTGTCTGTGGAAGGCGGAAACGGCTGCTGGGGCCCATG
TTCTTGCGAAGGGACCTAACTAAGCCCGCCATGTCTGGGGGCTTCGAGCTGCAGCCGCTGGACG
GCGGCCCCCGGGTGGCCCTGGCGCCCGGGGAGACGGTGATCGGTCGCGGGCCGCTGCTGGGAAT
AACTGACAAGAGAGTATCCAGAAGACATGCCATTCTTGAGGTAGTGGGTGGTCAGCTTCGAATC
AAACCGATACACACAAATCCATGTTTTTATCAGTCTTCTGAGAAAAGCCAACCCTTACCAATGA
AGACAAATCTGTGGCGCTGGTTGAATCCTGGAGATAGTTTTTCTTTGTTAGTTGACAAGTACAT
TTTTCGTGTTTTTGCTACACAATCGGAAACAGACATGGAATGCACATTGCGAAACAGCCAAATG
CTTGAGGAAGATAATATATTGAATGAAGTACCAAAATCTCCTGTGACTAAAAGTTTGCCTGATA
AGACAACTGGCACCTCACAGGTAGAAAGAAGCACAGAACTACCCAAGACCCAGACTACTACCAC
TAATAGTGTGTCTTTCCTAGGTGAATGTAGAGACTTCAGTAAGCAACAGTCAAACCCTGCCCAG
AGGAAAAGAGTTCTTCCAGCTTGGATGTTAGCAGAGAATTTAAGTGATCAAAACCTTTCAGCAT
CTGTCATCAGTGGAGATAATAATATAATCCAAGAATGTGGAAAAGAAGGAATCTCCAAAGATAA
AACCCAAGTAAACATGACCCAGCAAAGAAAGCGAGTAATTTCATCAGGAAATTCAGAAAGTATA
TCAGCAGAAGATGATGCAGGAAAAAAGTGCAAAAATGCTGATCAAGAAGAGTCTGTCATTTCAT
CCAAGGAAATGCCAGAATCATTTTCTACAGTTACTCTGAGTAATACAGATATAAATACTATGAA
GACAAATACACAGAGAAATGAAATTCCAGTAGAGGAGCTTGGTAATGTTTCTGAACATAAAATC
ATAACTAAAGGAACACCAAATAAAGAGGACAAGGCAGTGAGTTATTCTGAAAGTTATTCGAGTG
TTCCAGGCAGGTCATCCTGTGGTGAGTCTCAAGGATCTCATCCCGAGTCTACCTCTGATTCCTT
CAGTCCTGAAACTTTACATTCAAAAACAAGTGATTCAGTTCCAGGAGGTTCCGAAGAAAACAGA
GTCAAGAGAACATCCTGCATGTATGGGGCAAACTGCTACAGGAAGAATCCTGTTCATTTTCAAC
ACTTCAGCCACCCTGGTGATAGTGATTATGGAAGTGTACAAATCATAGATCAAGATGAAACTGA
TGACCGGCCTGAATGCCCCTATGGAGCATCTTGTTATAGGAAGAATCCCCAGCACAAGATAGAA
TATAGACATAGTACTCTTACAGATGAAGATAATGATGATGTTGGACAACCCAATGAGTCTGACC
TGAATGACAGCTTTATAGATGATGAAGAAGAAGAATATGAGCCAACAGATGAAGATTCTGACTG
GGAACCAGAGAAGGAAGACCAAGAGAAGGAAGATGTGGAAGAGCTTTTGAAGGAAGCAAAAAAG
TTTATGAAAAGAAAAAAATAACTCTTTTCTGCAATAATATAGGGCTCAATTTCAGGAACTAAGG
TGGTACTAGAGTGATCATTATTTTCTTTCTTTTGATAGCTACAACTTTTGCTATTGACTTTTTG
CAAGTAAAATATTGAAATGTCAGCCATTAAGGTAGTAGGTGGAATTTATTTTGTTGCCTTACTT
AAGCACTTACTAGTAGAAAGCAGATAGAGGTTAAAGAGGAATCAAATTTTCCCTGTACTTTGTA
TATTGATAATAAAAAGTAAAAGCCTTGGTTGT

hide sequence

RefSeq Acc Id:

XM_040271101 ⟹ XP_040127035

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024406292	15,609,577 - 15,713,285 (-)	NCBI

Protein Sequences


Protein RefSeqs	XP_021579993	(Get FASTA)	NCBI Sequence Viewer
	XP_040127035	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000013149.3
GenBank Protein	KAG3267190	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	XP_021579993 ⟸ XM_021724318
- Peptide Label:	isoform X2
- UniProtKB:	I3MND1 (UniProtKB/TrEMBL)
- Sequence:	show sequence MFLRRDLTKPAMSGGFELQPLDGGPRVALAPGETVIGRGPLLGITDKRVSRRHAILEVVGGQLR IKPIHTNPCFYQSSEKSQPLPMKTNLWRWLNPGDSFSLLVDKYIFRVFATQSETDMECTLRNSQ MLEEDNILNEVPKSPVTKSLPDKTTGTSQVERSTELPKTQTTTTNSVSFLGECRDFSKQQSNPA QRKRVLPAWMLAENLSDQNLSASVISGDNNIIQECGKEGISKDKTQVNMTQQRKRVISSGNSES ISAEDDAGKKCKNADQEESVISSKEMPESFSTVTLSNTDINTMKTNTQRNEIPVEELGNVSEHK IITKGTPNKEDKAVSYSESYSSVPGRSSCGESQGSHPESTSDSFSPETLHSKTSDSVPGGSEEN RVKRTSCMYGANCYRKNPVHFQHFSHPGDSDYGSVQIIDQDETDDRPECPYGASCYRKNPQHKI EYRHSTLTDEDNDDVGQPNESDLNDSFIDDEEEEYEPTDEDSDWEPEKEDQEKEDVEELLKEAK KFMKRKK hide sequence

RefSeq Acc Id:	XP_040127035 ⟸ XM_040271101
- Peptide Label:	isoform X1

RefSeq Acc Id:

ENSSTOP00000013149 ⟸ ENSSTOT00000014679

Protein Domains

Aprataxin and PNK-like factor PBZ PNK FHA

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000014677	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000014679.3	UniProtKB/TrEMBL
Gene3D-CATH	2.60.200.20	UniProtKB/TrEMBL
InterPro	APLF	UniProtKB/TrEMBL
	APLF_PBZ	UniProtKB/TrEMBL
	FHA_2	UniProtKB/TrEMBL
	SMAD_FHA_dom_sf	UniProtKB/TrEMBL
NCBI Gene	Aplf	ENTREZGENE
PANTHER	APRATAXIN AND PNK-LIKE FACTOR	UniProtKB/TrEMBL
	PTHR21315	UniProtKB/TrEMBL
Pfam	FHA_2	UniProtKB/TrEMBL
	zf-CCHH	UniProtKB/TrEMBL
Superfamily-SCOP	SSF49879	UniProtKB/TrEMBL
UniProt	I3MND1	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

RGD Manual Annotations

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Imported Disease Annotations - ClinVar

RGD Manual Annotations