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AFG3L1P Gene

pseudogene   GIFtS: 26
GCID: GC16P090041

AFG3-Like AAA ATPase 1, Pseudogene

(Previous names: AFG3 ATPase family gene 3-like 1 (S. cerevisiae), pseudogene,...)
(Previous symbols: AFG3, AFG3L1)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
AFG3-Like AAA ATPase 1, Pseudogene1 2
AFG31 2 5
AFG3L11 2 5
AFG3 ATPase Family Gene 3-Like 1 (S. Cerevisiae), Pseudogene1
AFG3 ATPase Family Member 3-Like 1 (S. Cerevisiae), Pseudogene1

External Ids:    HGNC: 3141   Entrez Gene: 1722   Ensembl: ENSG000002239597   OMIM: 6030205   
ORGUL members:         

Export aliases for AFG3L1P gene to outside databases

Previous GC identifer: GC16P090039


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for AFG3L1P Gene:
AFG3L1P (AFG3-like AAA ATPase 1, pseudogene) is a pseudogene, and is affiliated with the antisense RNA class.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000016.9  NC_018927.2  NT_010498.16  
Regulatory elements:
   Search for regulatory transcription factor binding sites for AFG3L1P
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat AFG3L1P


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16q24.3   Ensembl cytogenetic band:  16q24.3   HGNC cytogenetic band: 16q24.3

AFG3L1P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
AFG3L1P gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P090041:  view genomic region     (about GC identifiers)

Start:
90,038,988 bp from pter      End:
90,068,569 bp from pter
Size:
29,582 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for AFG3L1P

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
AATP: ATPases / AAA-type

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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Interactions:

    Search GeneGlobe Interaction Network for AFG3L1P

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for AFG3L1P



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for AFG3L1P gene (2 alternative transcripts): 
NM_001031805.1  NM_001132.2  

Unigene Cluster for AFG3L1P:

AFG3 ATPase family member 3-like 1 (S. cerevisiae), pseudogene
Hs.534773  [show with all ESTs]
Unigene Representative Sequence: NR_003226
17 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000431757 ENST00000429663 ENST00000418696(uc002fpw.1) ENST00000450026
ENST00000457926(uc002fpu.1 uc002fqa.1) ENST00000436447 ENST00000423742
ENST00000437774(uc002fpt.1 uc002fpv.1) ENST00000557444(uc002fpx.1 uc002fqb.1)
ENST00000421164(uc002fps.1 uc002fpy.1 uc002fpz.1) ENST00000423684
ENST00000421780 ENST00000388970 ENST00000458301 ENST00000355531 ENST00000427658(uc002fqc.1)
ENST00000454997(uc002fqd.1)
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Additional mRNA sequence: 

AF329691.1 AF329692.1 AF329693.1 AF329694.1 AJ001495.1 AK056488.1 AK090856.1 AK091293.1 
AK091727.1 AK126911.1 AK127143.1 AK128352.1 AK128804.1 BC077734.1 NR_003226.1 NR_003227.1 
NR_003228.1 

Selected DOTS entries (see all 28):

DT.101982307  DT.120720828  DT.95272640  DT.100024043  DT.100024045  DT.99999442  DT.100675254  DT.310423 
DT.40212010  DT.310424  DT.97771816  DT.100755526  DT.120720840  DT.91816887  DT.100024046  DT.97831337 
DT.97839887  DT.120720972  DT.120721014  DT.97839889  DT.100755529  DT.111280  DT.120720641  DT.120720881 

Selected AceView cDNA sequences (see all 88):

AA350737 AF329692 BC021245 BM720338 AI204538 AI215191 BM986843 AK128352 
BC045753 NM_001132 AI693214 CA433594 AJ001495 BM803134 BF110425 AF329691 
BG654568 BM807451 BM051047 AK126911 AA877574 AI033057 AK091293 AA318028 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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AFG3L1P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AGGTGAGTGG
AFG3L1P Expression
About this image

AFG3L1P Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.534773
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for AFG3L1P gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Afg3l15 AFG3(ATPase family gene 3)-like 1 (yeast)   --   8 (72.10 cM) 123477903 


ENSEMBL Gene Tree for AFG3L1P (if available)
TreeFam Gene Tree for AFG3L1P (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for AFG3L1P (see all 788)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 16 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1469307481,2
--90041329(+) TGTCCC/TCTGCA 3 -- int10--------
rs1134980281,2
C,F--90041440(+) AGAGGT/CTAGTG 3 -- int13Minor allele frequency- C:0.02CSA WA NA 240
rs1378603601,2
--90041685(+) TTGCAG/TAAAAC 3 -- int10--------
rs1163127041,2
F--90041782(+) AATCAC/GAAAAG 3 -- int11Minor allele frequency- G:0.01WA 118
rs740371501,2
C--90042167(+) AAACCC/GCCATC 3 -- int13Minor allele frequency- G:0.11WA NA 240
rs1836254901,2
--90042216(+) GCTCTG/TTGTCA 3 -- int10--------
rs1861692031,2
--90042236(+) TGCCAC/TTGGTG 3 -- int10--------
rs116434951,2
C,F,H--90042268(+) GATTTC/TGTTCA 3 -- int14Minor allele frequency- T:0.15NA EA 128
rs71952261,2
C,F,A,H--90042276(+) TCACGA/GTGTGG 3 -- int18Minor allele frequency- G:0.16NA WA CSA EA 250
rs1910181281,2
--90042285(+) GGAATC/TGTTTG 3 -- int10--------

HapMap Linkage Disequilibrium report for AFG3L1P (90038988 - 90068569 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for AFG3L1P (see all 16):    About this table    
Variant IDTypeSubtypePubMed ID
esv3689CNV Deletion18987735
esv2136699CNV Deletion18987734
esv2664835CNV Deletion23128226
nsv103059CNV Insertion16902084
dgv3009n71CNV Loss21882294
nsv907445CNV Loss21882294
nsv907443CNV Loss21882294
nsv103116CNV Loss16902084
nsv482951CNV Loss15286789
nsv471119CNV Loss18288195

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing AFG3L1P
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 603020    OMIM disorders: --


Find genes that share disorders with AFG3L1P           About GenesLikeMe


Export disorders for AFG3L1P gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for AFG3L1P gene integrated from 10 sources:
(articles sorted by number of sources associating them with AFG3L1P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Molecular and functional analyses of the human and mouse genes encoding AFG3L1, a mitochondrial metalloprotease homologous to the human spastic paraplegia protein. (PubMed id 11549317)1, 3, 9 Kremmidiotis G....Callen D.F. (Genomics 2001)
  2. Chromosomal locations of three human nuclear genes (RPSM12, TUFM, and AFG3L1) specifying putative components of the mitochondrial gene expression apparatus. (PubMed id 9545647)1, 3, 9 Shah Z.H....Jacobs H.T. (Genomics 1998)
  3. The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. (PubMed id 21555518)1 Warnatz H.J....Yaspo M.L. (J. Biol. Chem. 2011)
  4. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
  5. Genome-wide association study identifies three loci associated with melanoma risk. (PubMed id 19578364)1 Bishop D.T....Bishop J.A. (Nat. Genet. 2009)
  6. Variable and tissue-specific subunit composition of mitochondrial m- AAA protease complexes linked to hereditary spastic paraplegia. (PubMed id 17101804)1 Koppen M.... Langer T. (Mol. Cell. Biol. 2007)
  7. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  10. Regulation of OPA1 processing and mitochondrial fusion by m-AAA protease isoenzymes and OMA1. (PubMed id 20038678)9 Ehses S....Langer T. (J. Cell Biol. 2009)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 172 HGNC: 314 AceView: AFG3L1 Ensembl:ENSG00000223959 euGenes: HUgn172
ECgene: AFG3L1P H-InvDB: AFG3L1P

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for AFG3L1P Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for AFG3L1P gene:
Search GeneIP for patents involving AFG3L1P

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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