RetrogeneDB ID:

retro_pvam_250

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_2167:121864..123169(-)
Located in intron of:ENSPVAG00000016473
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPD1
Ensembl ID:ENSPVAG00000008306
Aliases:None
Description:heat shock 60kDa protein 1 (chaperonin) [Source:HGNC Symbol;Acc:5261]


Retrocopy-Parental alignment summary:






>retro_pvam_250
GAAGGCTTTGAGAAGATTAGCAAAGGTGCTGATCCAGTAGAAATCAAGAGATGTGTGATGTTCACTGTTGATGCTATACT
TGCTGAACTTAAGAAGCAGTATAAACTTGTGACAACCCCTTAAGAAATTGCTCAGTTTGCTAAGATTTCTGCAAATGGAG
AGAAAGAAATTGGCAACATTATTTCTGATGCAATGAAGAAGATTGGAAGCAAGGGTGTCATCACAGTAAAGAATAGAAAA
ACACTAAATGTTAAATTAGAAATTATTGAAAGCATGAAGTTTGATCAAGATTATATTTCTCTATACTTTATTAATACAAC
TAAAGGTTAGAAATGTGAATTCCAAGAAGTCTATGTTCTACTGAGTGAAAAGAAAATTGCTAGTGTCCAGTTCAGTGTAC
CTGCTCTTGAAATTGCTACTGCCCATCATAAGCCCTTGGTCATCCTTGCTAAAGATGTTAATGGAGAAGCTCTCATTTTG
AATAAGCTAAAAGTTGGTCTTCCAGTTGTAGCAGTTAAAGTTCCAGGTTTTGATGACAGTAGAAAGAATCAGCTTAAAGA
CATGGCTATTGCTACTGCTGGTGAAGTGTTTGGAAAAGAAAGACTGACTCTAAATCTTGAATGTACTCAGCCTCAGACTT
AGGAAAAGCTGGAGAGGTCATTGTGACCAATGCTCTTGATGATGCCATGCTCTTGAAAAGAAAAGGTGACAAGGCTCAAA
GCAAAAAACGTATTCAAGAAACCCACTGAGCAGTTAGAAAATACAACTCGTGAATATAAAAAGGAAAAACTAAATGAACA
TCTGGCAAAACTCTCAGATGGAGTAACCGTGATAAAAGTTTGTGAGAGAAGTGATATTGAAGTGAATGAAAAGAAGGACA
GGGTAAGAGATACCCTCAAAGCTACACAAGCTGCTACTGAAGGAGGCATCATCTGGGAGGAGGTTGTGCCCTGCTTTGGT
GTATCCCAGCTTGGACTAATTAATGCCAGCTAATGAAGGTCAAAAATTGGTATAAAAATTATTAAGAAAACACTTAAAAT
TCTTGCAATGACCATTGCTAAGAATGCAGCTGTTGAGGGACTGTTGATAGTTGAGCAATACACAAAATTCCTCAGAAGAT
GGTTTTGATGCTATGTTTGGAGATTTTGTGTATATAGTGGAAAAAGGAATCATTGATCCAACTAAGGTTGTAAGAATTAT
TTTACTGGATGCTGCTGGAGTGGCGTATCTGTTGGCTAAAGCAGAAGTTGTAGTCACAAAAAATCCTAATAAGAGAAAGA
CCCTGGAATGGGTAGAATGGGAGGT

ORF - retro_pvam_250 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.83 %
Parental protein coverage: 76.31 %
Number of stop codons detected: 3
Number of frameshifts detected: 7


Retrocopy - Parental Gene Alignment:

ParentalEGFEKISKGANPVEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGR
EGFEKISKGA.PVEI.R.VM..VDA..AELKKQ.K.VTTP.EIAQ.A.ISANG.KEIGNIISDAMKK.G.
RetrocopyEGFEKISKGADPVEIKRCVMFTVDAILAELKKQYKLVTTP*EIAQFAKISANGEKEIGNIISDAMKKIGS
ParentalKGVITVKDGKTLNDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIAN
KGVITVK..KTLN..LEIIE.MKFD..YIS.YFINT.KG.KCEFQ..YVLLSEKKI.SVQ..VPALEIA.
RetrocopyKGVITVKNRKTLNVKLEIIESMKFDQDYISLYFINTTKG*KCEFQEVYVLLSEKKIASVQFSVPALEIAT
ParentalAHRKPLVIIAEDVDGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLE
AH.KPLVI.A.DV.GEAL....LN.LKVGL.VVAVK.PGF.D.RKNQLKDMAIAT.G.VFG.E.LTLNLE
RetrocopyAHHKPLVILAKDVNGEAL---ILNKLKVGLPVVAVKVPGFDDSRKNQLKDMAIATAGEVFGKERLTLNLE
ParentalDVQ-SHDLGKVGEVIVTK--DDAMLLKGKGDKAQIEKRIQEI-MEQLDTTTSEYEKEKLNERLAKLSDGV
..Q...DLGK.GEVIVT...DDAMLLK.KGDKAQ..KRIQE...EQL..TT.EY.KEKLNE.LAKLSDGV
RetrocopyCTQ<ASDLGKAGEVIVTNALDDAMLLKRKGDKAQSKKRIQET>TEQLENTTREYKKEKLNEHLAKLSDGV
ParentalAVLKVGGTSDVEVNEKKDRVTDALNATRAAVEEGIV-LGGGCALLRCIPA-LDSLTPANEDQ-KIGIEII
.V.KV...SD.EVNEKKDRV.D.L.AT.AA.E.GI..LGGGCALL.CIPA.LD.L.PANE.Q.KIGI.II
RetrocopyTVIKVCERSDIEVNEKKDRVRDTLKATQAATEGGII<LGGGCALLWCIPA<LD*LMPANEGQ<KIGIKII
ParentalKKALKIPAMTIAKNAGVEGSLIVEK-IMQSSSEVGYDAMLGDFVNMVEKGIIDPTKVVRTALLDAAGVAS
KK.LKI.AMTIAKNA.VEG.LIVE.....SS...G.DAM.GDFV..VEKGIIDPTKVVR..LLDAAGVA.
RetrocopyKKTLKILAMTIAKNAAVEGLLIVEQ>TQNSSED-GFDAMFGDFVYIVEKGIIDPTKVVRIILLDAAGVAY
ParentalLLTTAEAVVTEIPKE-EKDPGMGGMGG
LL..AE.VVT..P...EKDPGMG.MGG
RetrocopyLLAKAEVVVTKNPNK<EKDPGMGRMGG

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_250 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 17 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Choloepus hoffmanni ENSCHOG000000074015 retrocopies
retro_chof_1105, retro_chof_1300, retro_chof_1822, retro_chof_2000, retro_chof_2397,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Echinops telfairi ENSETEG000000091844 retrocopies
retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Loxodonta africana ENSLAFG000000000531 retrocopy
retro_lafr_476,
Macropus eugenii ENSMEUG000000119872 retrocopies
retro_meug_1688, retro_meug_224,
Myotis lucifugus ENSMLUG000000008714 retrocopies
retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta ENSMMUG000000104891 retrocopy
retro_mmul_83,
Monodelphis domestica ENSMODG000000122893 retrocopies
retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furoENSMPUG000000078183 retrocopies
retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pteropus vampyrus ENSPVAG00000008306 1 retrocopy
retro_pvam_250 ,
Rattus norvegicus ENSRNOG000000145259 retrocopies
retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Ictidomys tridecemlineatus ENSSTOG000000284701 retrocopy
retro_itri_224,
Tarsius syrichta ENSTSYG000000005136 retrocopies
retro_tsyr_1091, retro_tsyr_1181, retro_tsyr_1445, retro_tsyr_2082, retro_tsyr_395, retro_tsyr_804,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,


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