Aplf (aprataxin and PNKP like factor) - Rat Genome Database
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Gene: Aplf (aprataxin and PNKP like factor) Mus musculus
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Symbol: Aplf
Name: aprataxin and PNKP like factor
RGD ID: 1619131
MGI Page MGI
Description: Predicted to have DNA-(apurinic or apyrimidinic site) endonuclease activity; nuclease activity; and nucleotide binding activity. Involved in double-strand break repair and regulation of isotype switching. Predicted to localize to nucleoplasm and site of double-strand break. Orthologous to human APLF (aprataxin and PNKP like factor); PARTICIPATES IN ADP-ribosylation pathway, mono and poly-ribosylation; histone modification pathway; non-homologous end joining pathway of double-strand break repair; INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; benzo[a]pyrene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 2010301N04Rik; AI452191; aprataxin and PNK-like factor; apurinic-apyrimidinic endonuclease APLF
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39687,605,407 - 87,649,244 (-)NCBIGRCm39mm39
GRCm38687,628,425 - 87,672,237 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl687,628,424 - 87,672,193 (-)EnsemblGRCm38mm10GRCm38
MGSCv37687,578,423 - 87,622,162 (-)NCBIGRCm37mm9NCBIm37
MGSCv36687,594,070 - 87,637,788 (-)NCBImm8
Celera689,562,818 - 89,606,576 (-)NCBICelera
Cytogenetic Map6D1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12520002   PMID:15489334   PMID:15782199   PMID:16141072   PMID:16141073   PMID:17277741  
PMID:21211721   PMID:21873635   PMID:22922362   PMID:27875275   PMID:30595499   PMID:32098917   PMID:32325033  


Genomics

Comparative Map Data
Aplf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39687,605,407 - 87,649,244 (-)NCBIGRCm39mm39
GRCm38687,628,425 - 87,672,237 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl687,628,424 - 87,672,193 (-)EnsemblGRCm38mm10GRCm38
MGSCv37687,578,423 - 87,622,162 (-)NCBIGRCm37mm9NCBIm37
MGSCv36687,594,070 - 87,637,788 (-)NCBImm8
Celera689,562,818 - 89,606,576 (-)NCBICelera
Cytogenetic Map6D1NCBI
APLF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl268,467,572 - 68,655,862 (+)EnsemblGRCh38hg38GRCh38
GRCh38268,467,585 - 68,580,162 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37268,694,717 - 68,807,294 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37268,694,691 - 68,839,361 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36268,548,246 - 68,660,798 (+)NCBINCBI36hg18NCBI36
Build 34268,606,392 - 68,718,944NCBI
Celera268,544,671 - 68,657,741 (+)NCBI
Cytogenetic Map2p13.3NCBI
HuRef268,431,541 - 68,543,835 (+)NCBIHuRef
CHM1_1268,624,013 - 68,736,628 (+)NCBICHM1_1
Aplf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24120,070,471 - 120,122,656 (-)NCBI
Rnor_6.0 Ensembl4119,514,840 - 119,568,736 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04119,514,822 - 119,568,764 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04184,816,979 - 184,819,739 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.04184,767,521 - 184,809,501 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44121,796,926 - 121,849,410 (-)NCBIRGSC3.4rn4RGSC3.4
Celera4109,037,717 - 109,083,976 (-)NCBICelera
Cytogenetic Map4q34NCBI
Aplf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542416,336,228 - 16,448,766 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542416,338,546 - 16,449,074 (-)NCBIChiLan1.0ChiLan1.0
APLF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A69,632,459 - 69,744,611 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A69,632,459 - 69,744,611 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A68,509,314 - 68,629,192 (+)NCBIMhudiblu_PPA_v0panPan3
APLF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1067,454,356 - 67,521,761 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11067,454,500 - 67,522,659 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Aplf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493649112,857,928 - 12,961,709 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APLF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl373,752,106 - 73,831,075 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1373,752,115 - 73,831,158 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2377,287,005 - 77,362,138 (-)NCBISscrofa10.2Sscrofa10.2susScr3
APLF
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11438,539,398 - 38,636,666 (-)NCBI
ChlSab1.1 Ensembl1438,540,084 - 38,636,569 (-)Ensembl
Aplf
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247624,727,834 - 4,847,779 (-)NCBI

Position Markers
AI452191  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38687,629,882 - 87,629,994UniSTSGRCm38
MGSCv37687,579,876 - 87,579,988UniSTSGRCm37
Celera689,564,271 - 89,564,383UniSTS
Cytogenetic Map6D1UniSTS
Whitehead/MRC_RH6905.37UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25440480Moaq2_mmodifier of alien QTL 2 (mouse)61117500000Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139100000Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396656149Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396656149Mouse
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396656149Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396656149Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63866962592607450Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645314059128835032Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46935985136423692Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648720000125360000Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648720000148450000Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648726556125356785Mouse
1357683Igf1sl1_mIGF-1 serum levels 1 (mouse)Not determined652161713116155267Mouse
4141028Mclr_mmethylcholanthrene lymphoma resistance (mouse)Not determined5437342788379171Mouse
15039373Adip28_madiposity 28 (mouse)65630821190308211Mouse
15039375Bw41_mbody weight QTL 41 (mouse)65630821190308211Mouse
1558977Skmw10_mskeletal muscle weight 10 (mouse)Not determined65844758392447710Mouse
10043972Obq28_mobesity QTL 28 (mouse)Not determined65854043392540433Mouse
1301740Bwq2_mbody weight QTL 2 (mouse)Not determined66005768094057799Mouse
1301369Im4_mimmunoregulatory 4 (mouse)Not determined66348473897484905Mouse
1300650Bw18_mbody weight QTL 18 (mouse)Not determined666713869100714031Mouse
1301876Bits2_mbitterness sensitivity 2 (mouse)Not determined670425898104426034Mouse
1301813Skl3_mskeletal size (tail length) 3 (mouse)Not determined670425898104426034Mouse
1301034Egrm2_mearly growth rate (mouse)Not determined670425898104426034Mouse
1302020Bbaa20_mB.burgdorferi-associated arthritis 20 (mouse)Not determined67132262193464093Mouse
1300869Stheal5_msoft tissue heal 5 (mouse)Not determined671575060105575178Mouse
1300954Fcsa1_mfemoral cross-sectional area 1 (mouse)Not determined671981024105981170Mouse
1301521Pas1c_mpulmonary adenoma susceptibility 1c (mouse)Not determined671981024105981170Mouse
13506930Recrq9_mrecombination rate in male meiosis QTL 9 (mouse)673500000134700000Mouse
1301320Ots1_movarian teratoma susceptibility 1 (mouse)Not determined675447583104503555Mouse
1301571Arrd1_mage-related retinal degeneration 1 (mouse)Not determined67554435692607450Mouse
1300674Nidd3n_mnon-insulin-dependent diabetes mellitus 3 in NSY (mouse)Not determined67554435694225955Mouse
10412195Efw_mepididymal fat weight (mouse)Not determined67554435694225955Mouse
10043901Pfat5_mpredicted fat percentage 5 (mouse)Not determined675607306109607450Mouse
10412208Cypr4_mcytokine production 4 (mouse)Not determined675716503109716697Mouse
1357875Pfat2_mpredicted fat percentage 2 (mouse)Not determined676463949110464093Mouse
14697704Stsl4_mSalmonella typhimurium susceptibility locus 4 (mouse)67710000090000000Mouse
13824985Alh1_mamplitude of lateral head displacement 1 (mouse)67800000097000000Mouse
4141376Dbm1_mdiabetes modifier 1 (mouse)Not determined678629504121115387Mouse
14696731Pairq1_mP. aeruginosa infection resistance QTL 1 (mouse)681500000102200000Mouse
10043864T2dm4sa_mtype 2 diabetes mellitus 4 in SMXA RI mice (mouse)Not determined683713869147052561Mouse
11251720Ewc4_methanol withdrawal and consumption 4 (mouse)684122513118122513Mouse
1301687Mnic2_mmacronutrient intake (mouse)Not determined686806805113544602Mouse
1301744Hdlq11_mHDL QTL 11 (mouse)Not determined687503360121503555Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1048
Count of miRNA genes:368
Interacting mature miRNAs:421
Transcripts:ENSMUST00000032130, ENSMUST00000065997
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000032130   ⟹   ENSMUSP00000032130
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl687,629,749 - 87,672,193 (-)Ensembl
RefSeq Acc Id: ENSMUST00000065997   ⟹   ENSMUSP00000066232
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl687,628,424 - 87,672,147 (-)Ensembl
RefSeq Acc Id: ENSMUST00000203209   ⟹   ENSMUSP00000145358
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl687,629,744 - 87,672,064 (-)Ensembl
RefSeq Acc Id: ENSMUST00000203776
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl687,651,091 - 87,672,129 (-)Ensembl
RefSeq Acc Id: NM_001170489   ⟹   NP_001163960
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39687,605,411 - 87,649,150 (-)NCBI
GRCm38687,628,429 - 87,672,168 (-)NCBI
MGSCv37687,578,423 - 87,622,162 (-)RGD
Celera689,562,818 - 89,606,576 (-)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001372332   ⟹   NP_001359261
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39687,605,407 - 87,649,143 (-)NCBI
GRCm38687,628,425 - 87,672,161 (-)NCBI
RefSeq Acc Id: NM_024251   ⟹   NP_077213
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39687,605,411 - 87,649,150 (-)NCBI
GRCm38687,628,429 - 87,672,168 (-)NCBI
MGSCv37687,578,423 - 87,622,162 (-)RGD
Celera689,562,818 - 89,606,576 (-)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006506656   ⟹   XP_006506719
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39687,606,725 - 87,649,244 (-)NCBI
GRCm38687,629,743 - 87,672,237 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006506657   ⟹   XP_006506720
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39687,606,725 - 87,646,405 (-)NCBI
GRCm38687,629,743 - 87,669,429 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_077213   ⟸   NM_024251
- Peptide Label: isoform 2
- UniProtKB: Q9D842 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001163960   ⟸   NM_001170489
- Peptide Label: isoform 1
- UniProtKB: Q9D842 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006506719   ⟸   XM_006506656
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006506720   ⟸   XM_006506657
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001359261   ⟸   NM_001372332
- Peptide Label: isoform 3
RefSeq Acc Id: ENSMUSP00000145358   ⟸   ENSMUST00000203209
RefSeq Acc Id: ENSMUSP00000032130   ⟸   ENSMUST00000032130
RefSeq Acc Id: ENSMUSP00000066232   ⟸   ENSMUST00000065997
Protein Domains
FHA-like   FHA_2

Promoters
RGD ID:6839233
Promoter ID:MM_KWN:46774
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:AK054052_E230015B07RIK,   ENSMUST00000095740,   NM_001170489,   NM_024251,   UC009CTS.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36687,621,866 - 87,622,502 (+)MPROMDB
RGD ID:6890336
Promoter ID:EPDNEW_M8619
Type:initiation region
Name:Aplf_1
Description:Mus musculus aprataxin and PNKP like factor , transcript variant2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38687,672,161 - 87,672,221EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1919353 AgrOrtholog
Ensembl Genes ENSMUSG00000030051 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000032130 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000066232 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000145358 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000032130 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000065997 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000203209 UniProtKB/TrEMBL
InterPro APLF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  APLF_PBZ UniProtKB/Swiss-Prot
  FHA_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FHA_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMAD_FHA_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:72103 UniProtKB/Swiss-Prot
MGD MGI:1919353 ENTREZGENE
NCBI Gene 72103 ENTREZGENE
PANTHER PTHR21315 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FHA_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-CCHH UniProtKB/Swiss-Prot
PhenoGen Aplf PhenoGen
Superfamily-SCOP SSF49879 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0N4SW39_MOUSE UniProtKB/TrEMBL
  APLF_MOUSE UniProtKB/Swiss-Prot
  Q8BVD9_MOUSE UniProtKB/TrEMBL
  Q9D842 ENTREZGENE
UniProt Secondary Q8BZL5 UniProtKB/Swiss-Prot
  Q99LX6 UniProtKB/Swiss-Prot