RetrogeneDB ID:

retro_pvam_1333

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:scaffold_6263:50433..51422(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KPNA2
Ensembl ID:ENSPVAG00000004976
Aliases:None
Description:karyopherin alpha 2 (RAG cohort 1, importin alpha 1) [Source:HGNC Symbol;Acc:6395]


Retrocopy-Parental alignment summary:






>retro_pvam_1333
TTTTCTGAGTTGGCTATCAAGTATGGTGCAGCTGACTCACTGTTGGCTCTTCTTGTAGTTCCTAATATGTCATCTTTAGC
ATGTGGTTACTTATGTAATGTTACCTGGACACTTTCAAACCTTTGTCTCAACAAGAATCCTGCACTCCTATTTGGTGCTG
ATGAGCAAATTCTTCCTACTTTAGTTTGTCTCCTGCATCATGATTAACCGGAAGTAGCAGAGAGCTGCTGGACCATTTCC
TACCGACTGATGGTCTAAATGAAGAGATGGAAATGGTCATGAAAATAGAAGTTGTGCCCCAATTTGTGAAGCTCCTAGGA
GCTACTGAATTGCCAATTGTGACTCCTACACTAAGAACCATAGGAAATATTGTCATTGAAATAGATGAACAGATGCAGAT
TGTAATAGATGCAGGGGCACTTGCAGTCTTTCCCAGCATCCTAATGAATTCCAAAACTAATATTCAGATGTAAGCTACAT
GAATAATATCAAACATCCCAGCTGGCTGCCAGGACCAGATACAGCAACTTGTAAATTATGGATTAGTCCTAGTCCTCATT
GGTATTTTCTCTCAGGTAGACTTTAAGACACAAAAAGAAGTCATATGGGCTGTGACCAAGTACACATGTGATGGGACAGT
TGAACAGATCATATTCCTCATTCATTGTGGCATAATAGAACCATTAATGAACCCATTAACTTTAAAAACTACCAAAATTA
TTCTGGTTATTCTGTATGTTATTTCAAATATCTTTTAGGCTGCTGAGAAACTAGGTGAAACTGAGAAATTTAGTATAATA
TTTGAAGAATGTGGAGGTTTGAACAAAATTGAAGCTCTATAAAACCATGAAAATAAGTCTATGTGTAAAACTTCATTAAA
CTTGAGTGAGAAATATTTCTCTGTAAAAGAAGATCAAGATGTGCCAGAAACTACCTCTGAAGGCTATACATTCTAAGATC
AGGATGGCACTCCTTGGACCTTTAATTTT

ORF - retro_pvam_1333 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.73 %
Parental protein coverage: 63.14 %
Number of stop codons detected: 6
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHDDP
F..L.IKYGA.D.LLALL.VP.MSSLACGYL.N.TWTLSNLC.NKNPA....A.EQILPTLV.LLHHD.P
RetrocopyFSELAIKYGAADSLLALLVVPNMSSLACGYLCNVTWTLSNLCLNKNPALLFGADEQILPTLVCLLHHD*P
ParentalEVLADSCWAISYL-TDGPNERIEMVVKTGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQVVIDA
EV.A.SCW.ISY..TDG.NE..EMV.K..VVPQ.VKLLGATELPIVTP.LR.IGNIV...DEQ.Q.VIDA
RetrocopyEV-AESCWTISYR<TDGLNEEMEMVMKIEVVPQFVKLLGATELPIVTPTLRTIGNIVIEIDEQMQIVIDA
ParentalGALAIFPSLLTNSKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLIGVLSKADFKTQKEAVWAVTNY
GALA.FPS.L.NSKTNIQ..AT...SNI.AG.QDQIQQ.VN.GLV..LIG..S..DFKTQKE..WAVT.Y
RetrocopyGALAVFPSILMNSKTNIQM*AT*IISNIPAGCQDQIQQLVNYGLVLVLIGIFSQVDFKTQKEVIWAVTKY
ParentalTSGGTVEQIVYLVRCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIE
T..GTVEQI..L..CGIIEPLMN.LT.K.TKIILVIL..ISNIF.AAEKLGETEK.SI..EECGGL.KIE
RetrocopyTCDGTVEQIIFLIHCGIIEPLMNPLTLKTTKIILVILYVISNIF*AAEKLGETEKFSIIFEECGGLNKIE
ParentalALQNHENESVYKASLNLIEKYFSVEEEEDQNVVPETTSEGYTFQVQDGTPGTFNF
AL.NHEN.S..K.SLNL.EKYFSV.E..D...VPETTSEGYTF..QDGTP.TFNF
RetrocopyAL*NHENKSMCKTSLNLSEKYFSVKEDQD---VPETTSEGYTF*DQDGTPWTFNF

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pteropus vampyrus was not studied using ChIP-Seq data.

EST - click to see more details

Pteropus vampyrus was not studied using EST data.

TSS - click to see more details

Pteropus vampyrus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pvam_1333 was not experimentally validated.

Retrocopy orthology:
Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 19 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG000000191516 retrocopies
retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Homo sapiens ENSG000001824811 retrocopy
retro_hsap_2950,
Gorilla gorilla ENSGGOG000000275352 retrocopies
retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Nomascus leucogenys ENSNLEG000000017493 retrocopies
retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pteropus vampyrus ENSPVAG00000004976 2 retrocopies
retro_pvam_1321, retro_pvam_1333 ,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,
Vicugna pacos ENSVPAG000000018553 retrocopies
retro_vpac_124, retro_vpac_162, retro_vpac_163,


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