Aplf (aprataxin and PNKP like factor) - Rat Genome Database

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Gene: Aplf (aprataxin and PNKP like factor) Rattus norvegicus
Analyze
Symbol: Aplf
Name: aprataxin and PNKP like factor
RGD ID: 1565557
Description: Predicted to enable several functions, including ADP-D-ribose modification-dependent protein binding activity; nuclease activity; and poly-ADP-D-ribose binding activity. Predicted to be involved in several processes, including DNA repair; DNA repair-dependent chromatin remodeling; and embryo implantation. Predicted to act upstream of or within positive regulation of DNA ligation and regulation of isotype switching. Predicted to be located in nucleoplasm. Predicted to be active in cytosol; nucleus; 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 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: aprataxin and PNK-like factor; LOC500247; RGD1565557; similar to RIKEN cDNA 2010301N04
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84121,627,800 - 121,679,980 (-)NCBIGRCr8
mRatBN7.24120,070,471 - 120,122,656 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4120,070,471 - 120,122,633 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4125,544,041 - 125,602,785 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04121,318,838 - 121,377,584 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04119,943,068 - 120,001,808 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04119,514,822 - 119,568,764 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4119,514,840 - 119,568,736 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04184,767,521 - 184,809,501 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.04184,816,979 - 184,819,739 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44121,796,926 - 121,849,410 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4109,037,717 - 109,083,976 (-)NCBICelera
Cytogenetic Map4q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Structures and Mechanisms of Enzymes Employed in the Synthesis and Degradation of PARP-Dependent Protein ADP-Ribosylation. Barkauskaite E, etal., Mol Cell. 2015 Jun 18;58(6):935-46. doi: 10.1016/j.molcel.2015.05.007.
2. Histone chaperones in nucleosome assembly and human disease. Burgess RJ and Zhang Z, Nat Struct Mol Biol. 2013 Jan;20(1):14-22. doi: 10.1038/nsmb.2461.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Lieber MR Annu Rev Biochem. 2010;79:181-211. doi: 10.1146/annurev.biochem.052308.093131.
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:17396150   PMID:18172500   PMID:21211721  


Genomics

Comparative Map Data
Aplf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84121,627,800 - 121,679,980 (-)NCBIGRCr8
mRatBN7.24120,070,471 - 120,122,656 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4120,070,471 - 120,122,633 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4125,544,041 - 125,602,785 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04121,318,838 - 121,377,584 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04119,943,068 - 120,001,808 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04119,514,822 - 119,568,764 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4119,514,840 - 119,568,736 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04184,767,521 - 184,809,501 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.04184,816,979 - 184,819,739 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44121,796,926 - 121,849,410 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4109,037,717 - 109,083,976 (-)NCBICelera
Cytogenetic Map4q34NCBI
APLF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38268,467,585 - 68,580,162 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl268,467,572 - 68,655,862 (+)EnsemblGRCh38hg38GRCh38
GRCh37268,694,717 - 68,807,294 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36268,548,246 - 68,660,798 (+)NCBINCBI36Build 36hg18NCBI36
Build 34268,606,392 - 68,718,944NCBI
Celera268,544,671 - 68,657,741 (+)NCBICelera
Cytogenetic Map2p13.3NCBI
HuRef268,431,541 - 68,543,835 (+)NCBIHuRef
CHM1_1268,624,013 - 68,736,628 (+)NCBICHM1_1
T2T-CHM13v2.0268,479,947 - 68,592,502 (+)NCBIT2T-CHM13v2.0
Aplf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39687,605,407 - 87,649,244 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl687,605,406 - 87,649,175 (-)EnsemblGRCm39 Ensembl
GRCm38687,628,425 - 87,672,237 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl687,628,424 - 87,672,193 (-)EnsemblGRCm38mm10GRCm38
MGSCv37687,578,423 - 87,622,162 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36687,594,070 - 87,637,788 (-)NCBIMGSCv36mm8
Celera689,562,818 - 89,606,576 (-)NCBICelera
Cytogenetic Map6D1NCBI
cM Map638.52NCBI
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
NHGRI_mPanPan1-v21257,836,254 - 57,947,492 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A57,838,385 - 57,951,427 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A68,509,314 - 68,629,192 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A69,632,459 - 69,744,611 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A69,632,459 - 69,744,611 (+)Ensemblpanpan1.1panPan2
APLF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11067,454,500 - 67,522,659 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1067,454,356 - 67,521,761 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1067,344,455 - 67,413,321 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01068,473,928 - 68,543,022 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1068,473,934 - 68,546,201 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11068,156,771 - 68,224,622 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01068,455,171 - 68,524,808 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01068,750,534 - 68,819,077 (+)NCBIUU_Cfam_GSD_1.0
Aplf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629215,609,577 - 15,713,285 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649112,857,785 - 12,962,376 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649112,857,928 - 12,961,709 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APLF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl373,752,118 - 73,831,035 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11438,539,398 - 38,636,666 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1438,540,084 - 38,636,569 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604573,339,984 - 73,456,338 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Aplf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247624,724,813 - 4,847,416 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247624,727,834 - 4,847,779 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Aplf
362 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:116
Count of miRNA genes:95
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000041234
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631689Scl4Serum cholesterol level QTL 41.90.008blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)495174120140174120Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)485253748148090731Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105789505150789505Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
1578655Bmd11Bone mineral density QTL 1111femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)490850165135850165Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470362013132642728Rat
738015Pia9Pristane induced arthritis QTL 94.50.048joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)480694870125694870Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473169846132642728Rat
634334Xhs3X-ray hypersensitivity QTL 310intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)484728680129854654Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
61476Aia3Adjuvant induced arthritis QTL 33.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)486730991131730991Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1641919Alc22Alcohol consumption QTL 220.0005drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)481192555126192555Rat
631662Hcar2Hepatocarcinoma resistance QTL 23.10.0003liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)478878504123878504Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2306899Bp338Blood pressure QTL 3380.071arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)481006124120102625Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
1578670Bss14Bone structure and strength QTL 1416.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)487327165132327165Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)485253748150276390Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4103194656148194656Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
12798527Anxrr58Anxiety related response QTL 584.110.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4119463257147278687Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1578662Bss15Bone structure and strength QTL 1519.6femur width (VT:1000666)femoral neck width (CMO:0001695)487327165132327165Rat

Markers in Region
D4Rat54  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24120,102,454 - 120,102,625 (+)MAPPERmRatBN7.2
Rnor_6.04119,546,804 - 119,546,974NCBIRnor6.0
Rnor_5.04184,799,503 - 184,799,673UniSTSRnor5.0
RGSC_v3.44121,828,905 - 121,829,076RGDRGSC3.4
RGSC_v3.44121,828,906 - 121,829,076UniSTSRGSC3.4
RGSC_v3.14122,073,386 - 122,073,557RGD
Celera4109,069,673 - 109,069,839UniSTS
RH 3.4 Map4710.5RGD
RH 3.4 Map4710.5UniSTS
RH 2.0 Map4739.9RGD
SHRSP x BN Map456.08RGD
Cytogenetic Map4q34UniSTS
D4Rat51  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24120,093,877 - 120,094,047 (+)MAPPERmRatBN7.2
Rnor_6.04119,538,229 - 119,538,396NCBIRnor6.0
Rnor_5.04184,790,928 - 184,791,095UniSTSRnor5.0
RGSC_v3.44121,820,331 - 121,820,498UniSTSRGSC3.4
RGSC_v3.44121,820,330 - 121,820,498RGDRGSC3.4
RGSC_v3.14122,064,812 - 122,064,979RGD
Celera4109,061,097 - 109,061,264UniSTS
RH 3.4 Map4710.1UniSTS
RH 3.4 Map4710.1RGD
RH 2.0 Map4741.5RGD
SHRSP x BN Map454.33RGD
FHH x ACI Map466.84RGD
Cytogenetic Map4q34UniSTS
RH131040  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24120,070,738 - 120,070,930 (+)MAPPERmRatBN7.2
Rnor_6.04119,515,090 - 119,515,281NCBIRnor6.0
Rnor_5.04184,767,789 - 184,767,980UniSTSRnor5.0
RGSC_v3.44121,797,193 - 121,797,384UniSTSRGSC3.4
Celera4109,037,985 - 109,038,176UniSTS
RH 3.4 Map4711.2UniSTS
Cytogenetic Map4q34UniSTS
RH134935  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24120,103,299 - 120,103,496 (+)MAPPERmRatBN7.2
Rnor_6.04119,547,649 - 119,547,845NCBIRnor6.0
Rnor_5.04184,800,348 - 184,800,544UniSTSRnor5.0
RGSC_v3.44121,829,751 - 121,829,947UniSTSRGSC3.4
Celera4109,070,514 - 109,070,710UniSTS
RH 3.4 Map4709.0UniSTS
Cytogenetic Map4q34UniSTS
AU049270  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24120,111,287 - 120,111,584 (+)MAPPERmRatBN7.2
Rnor_6.04119,555,431 - 119,555,725NCBIRnor6.0
Rnor_5.04184,808,130 - 184,808,424UniSTSRnor5.0
RGSC_v3.44121,837,808 - 121,838,102UniSTSRGSC3.4
Celera4109,078,505 - 109,078,799UniSTS
Cytogenetic Map4q34UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 7 45 54 87 92 45
Low 14 141 182 147 15 147 36 45 250 28 53 24
Below cutoff

Sequence


Ensembl Acc Id: ENSRNOT00000041234   ⟹   ENSRNOP00000043929
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4120,070,471 - 120,122,608 (-)Ensembl
Rnor_6.0 Ensembl4119,514,840 - 119,568,736 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000117709   ⟹   ENSRNOP00000095757
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4120,070,471 - 120,122,633 (-)Ensembl
RefSeq Acc Id: NM_001173382   ⟹   NP_001166853
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84121,627,800 - 121,679,932 (-)NCBI
mRatBN7.24120,070,471 - 120,122,608 (-)NCBI
Rnor_6.04119,514,822 - 119,568,722 (-)NCBI
Rnor_5.04184,767,521 - 184,809,501 (-)NCBI
Rnor_5.04184,816,979 - 184,819,739 (-)NCBI
Celera4109,037,717 - 109,083,976 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763076   ⟹   XP_008761298
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84121,627,801 - 121,679,976 (-)NCBI
mRatBN7.24120,070,472 - 120,122,652 (-)NCBI
Rnor_6.04119,514,822 - 119,568,763 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592824   ⟹   XP_017448313
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84121,627,801 - 121,679,978 (-)NCBI
mRatBN7.24120,070,472 - 120,122,653 (-)NCBI
Rnor_6.04119,514,822 - 119,568,764 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592825   ⟹   XP_017448314
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84121,636,116 - 121,679,980 (-)NCBI
mRatBN7.24120,078,796 - 120,122,656 (-)NCBI
Rnor_6.04119,523,153 - 119,568,764 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039108164   ⟹   XP_038964092
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84121,627,801 - 121,661,417 (-)NCBI
mRatBN7.24120,070,472 - 120,104,082 (-)NCBI
RefSeq Acc Id: XR_005503300
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84121,627,801 - 121,679,976 (-)NCBI
mRatBN7.24120,070,472 - 120,122,652 (-)NCBI
RefSeq Acc Id: NP_001166853   ⟸   NM_001173382
- UniProtKB: A6IB10 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761298   ⟸   XM_008763076
- Peptide Label: isoform X1
- UniProtKB: F6Q5G6 (UniProtKB/TrEMBL),   A6IB10 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448313   ⟸   XM_017592824
- Peptide Label: isoform X2
- UniProtKB: A0A8I6AU35 (UniProtKB/TrEMBL),   A6IB10 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017448314   ⟸   XM_017592825
- Peptide Label: isoform X3
- UniProtKB: A6IB10 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000043929   ⟸   ENSRNOT00000041234
RefSeq Acc Id: XP_038964092   ⟸   XM_039108164
- Peptide Label: isoform X4
Ensembl Acc Id: ENSRNOP00000095757   ⟸   ENSRNOT00000117709
Protein Domains
Aprataxin and PNK-like factor PBZ   PNK FHA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F6Q5G6-F1-model_v2 AlphaFold F6Q5G6 1-510 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13693223
Promoter ID:EPDNEW_R3747
Type:multiple initiation site
Name:Aplf_1
Description:aprataxin and PNKP like factor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04119,568,706 - 119,568,766EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565557 AgrOrtholog
BioCyc Gene G2FUF-43860 BioCyc
Ensembl Genes ENSRNOG00000043059 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041234.6 UniProtKB/TrEMBL
  ENSRNOT00000117709.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.200.20 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7383333 IMAGE-MGC_LOAD
InterPro APLF UniProtKB/TrEMBL
  FHA_2 UniProtKB/TrEMBL
  SMAD_FHA_domain UniProtKB/TrEMBL
  Znf_C2H2_APLF-like UniProtKB/TrEMBL
MGC_CLONE MGC:116357 IMAGE-MGC_LOAD
NCBI Gene 500247 ENTREZGENE
PANTHER APRATAXIN AND PNK-LIKE FACTOR UniProtKB/TrEMBL
  PTHR21315 UniProtKB/TrEMBL
Pfam FHA_2 UniProtKB/TrEMBL
  zf-CCHH UniProtKB/TrEMBL
PhenoGen Aplf PhenoGen
RatGTEx ENSRNOG00000043059 RatGTEx
Superfamily-SCOP SMAD_FHA UniProtKB/TrEMBL
UniProt A0A8I6AU35 ENTREZGENE, UniProtKB/TrEMBL
  A6IB10 ENTREZGENE, UniProtKB/TrEMBL
  F6Q5G6 ENTREZGENE, UniProtKB/TrEMBL
  Q4KLI5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-16 Aplf  aprataxin and PNKP like factor  RGD1565557  similar to RIKEN cDNA 2010301N04   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1565557  similar to RIKEN cDNA 2010301N04   RGD1565557_predicted  similar to RIKEN cDNA 2010301N04 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1565557_predicted  similar to RIKEN cDNA 2010301N04 (predicted)  LOC500247  similar to RIKEN cDNA 2010301N04  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500247  similar to RIKEN cDNA 2010301N04      Symbol and Name status set to provisional 70820 PROVISIONAL