RetrogeneDB ID:

retro_pvam_1190

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:scaffold_3906:31030..32050(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMC1
Ensembl ID:ENSPVAG00000010020
Aliases:None
Description:proteasome (prosome, macropain) 26S subunit, ATPase, 1 [Source:HGNC Symbol;Acc:9547]


Retrocopy-Parental alignment summary:






>retro_pvam_1190
ATTAAATACTGTCTTCACATAGAGGAAGAATTCATTAGAAATCAGGAACAAATGAGGCCTTTAGAAGAAAAGCAAGAGGA
GGAAAGATCAAAGATGGATGATCTGAGGGGGATCCCAATGCCAGTAGGAACCTCAGAAGAGACCTTTGATGACAGTCACA
CAATTGCGTCTACATCTGTGGGCTCAGAACTTTATGTTAGCGTTCTTTTATTTGTAGACAAGGATCTGCTGGAACCAGAC
TGCTTGGTCCTAATCAATCACAAGGTGCATGCCATGATAGAGATGCTGATGGATAACATGGATCCCTTGATCACAGTGAT
GAAGGTGGAAAAGTCCCTACAGGAGGCCTGTGCTGCAATTGGCAGGGTTAGACAATCAAATCCAGAAAATTAAGGAATCT
GTGGAGCTTCTTCTCACTCATCCTGGATATTATAAAGATGATTTAAAGCTCCCTGTGGGGGTCATTCTCTGTGACCCACC
TGGCACAGGTAAAACCTTATTAGCCAGAGCAGTAGCAAATCAAACCTCAGCTGCTTTCTAGAGCATGGTTGGCTCTGAAT
TTATTCAGAAATACCTAGGCAATGGGCCCAAACTCCTTCAGAAAAGAATGCAAGAACATGCACTATCTACTGTGTTTATT
GATGAAATTTATGCTATTAGGACAAAAAGATATGACTCAAATTCTGGTGATGAGAGAGAAATTTAGTGAACAATGTTGTA
ACTGTTGAACCAGTTAAATGGATTTGATTCAAGGAGAGACATAAAAGTTATCATGGCAGCAAACTAAATAGAAACTTTGA
ATCCAGTACTTATCAGACCAGTCTGCATTGACAGGAAAATCTAATTCCTCCTGCCTGAAGAAAAGACCAAGAAGCGTGTC
TTTCAGATCCACACAAGCAGAATGATGCTGGCCAGTGATGTGACACTGGATGATTTGATCAAGCTAAAAATGACTTCTCG
GGTGCTAATATCAAAGCAATCTATATGGAAGCTGGTCCAATGGCCTTGAGAAAACATAGA

ORF - retro_pvam_1190 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.12 %
Parental protein coverage: 78.18 %
Number of stop codons detected: 6
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILS
IK..L..EEEFIRNQEQM.PLEEKQEEERSK.DDLRG.PM.VGT.EE..DD.H.I.STSVGSE.YVS.L.
RetrocopyIKYCLHIEEEFIRNQEQMRPLEEKQEEERSKMDDLRGIPMPVGTSEETFDDSHTIASTSVGSELYVSVLL
ParentalFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIG-GLDNQIQEIKESVELPLT
FVDKDLLEP.C.VL.NHKVHA.I..LMD..DPL.TVMKVEK..QE..A.IG.GLDNQIQ.IKESVEL.LT
RetrocopyFVDKDLLEPDCLVLINHKVHAMIEMLMDNMDPLITVMKVEKSLQEACAAIG>GLDNQIQKIKESVELLLT
ParentalHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEE
HP.YY.....K.P.GVIL..PPGTGKTLLA.AVANQTSA.F...VGSE.IQKYLG.GPKL.........E
RetrocopyHPGYYKD-DLKLPVGVILCDPPGTGKTLLARAVANQTSAAF*SMVGSEFIQKYLGNGPKLLQKRM---QE
ParentalHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGR
HA.S.VFIDEI.AI.TKRYDSNSG.EREI..TML.LLNQL.GFDSR.D.KVIMA.N.IETL.P.LIRP..
RetrocopyHALSTVFIDEIYAIRTKRYDSNSGDEREI**TML*LLNQLNGFDSRRDIKVIMAAN*IETLNPVLIRPVC
ParentalIDRKIEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLI-MAKDDLSGADIKAICTEAGLMALRERR
IDRKI.F.LP.EKTKKR.FQIHTSRM.LA.DVTLDDLI..AK.D.SGA.IKAI..EAG.MALR..R
RetrocopyIDRKI*FLLPEEKTKKRVFQIHTSRMMLASDVTLDDLI<QAKNDFSGANIKAIYMEAGPMALRKHR

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_1190 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 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000018394 retrocopies
retro_amel_1536, retro_amel_1886, retro_amel_405, retro_amel_962,
Canis familiaris ENSCAFG000000175102 retrocopies
retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni ENSCHOG000000135951 retrocopy
retro_chof_1954,
Dasypus novemcinctus ENSDNOG000000064581 retrocopy
retro_dnov_2162,
Equus caballus ENSECAG000000036011 retrocopy
retro_ecab_355,
Echinops telfairi ENSETEG000000026611 retrocopy
retro_etel_580,
Felis catus ENSFCAG000000113108 retrocopies
retro_fcat_1444, retro_fcat_1559, retro_fcat_2015, retro_fcat_344, retro_fcat_614, retro_fcat_691, retro_fcat_713, retro_fcat_924,
Macropus eugenii ENSMEUG000000015261 retrocopy
retro_meug_623,
Myotis lucifugus ENSMLUG000000074712 retrocopies
retro_mluc_2490, retro_mluc_508,
Macaca mulatta ENSMMUG000000229901 retrocopy
retro_mmul_255,
Mustela putorius furoENSMPUG000000081504 retrocopies
retro_mputfur_1602, retro_mputfur_409, retro_mputfur_654, retro_mputfur_815,
Mus musculus ENSMUSG000000211783 retrocopies
retro_mmus_1517, retro_mmus_1826, retro_mmus_812,
Oryctolagus cuniculus ENSOCUG000000062314 retrocopies
retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii ENSOGAG000000323432 retrocopies
retro_ogar_3014, retro_ogar_367,
Pongo abelii ENSPPYG000000259489 retrocopies
retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pteropus vampyrus ENSPVAG00000010020 3 retrocopies
retro_pvam_1190 , retro_pvam_350, retro_pvam_500,
Tursiops truncatus ENSTTRG000000135821 retrocopy
retro_ttru_239,


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