RetrogeneDB ID:

retro_pvam_1487

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:scaffold_993:29362..30355(-)
Located in intron of:ENSPVAG00000016419
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LDHB
Ensembl ID:ENSPVAG00000002462
Aliases:None
Description:lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]


Retrocopy-Parental alignment summary:






>retro_pvam_1487
ATGGCAACTGTCAAGGGTGAGCTTATGAGTAATCTAACTTCAGAGGAGGGTGTTCATCGCAATAAGATCTCCATTATAGG
AACTGGATCGGTTGGCATGGCCTGTGCTATCAGCATCCTGCTTAAAGGCTTGAGTGATGAACTTGCCTTGGTGGACGCTT
CTGAAGACAAGGTGAAGGGCGAGACAATGGATCTTCAACATGGCAGTCCTTTCATGAAAATGCCAAATATTGTTTGCAGT
AAAGATTATCTTGTCACTGCAAACTCCAACGTCGTGGTTATCACAGCAGGTGCACGGCAGGAAAAAGGAGAAACTCGCCT
TAATTTAGTGCAGCGAAATGTGGCCATCTTTAAATCAATTATTTCTAATATTATTCAGTACAGCCCTCACTGCAAGCTGA
TTGTTGTTTCCAATCCAGTGGATATCTTAACTTACGTAGCCTGGAAGTTGAGTGAATTTCCCCAAAACCGTGTTATTGGA
AGTGGTTGTAATCTGGACACTGCCCGTTTTCGTTTCTTGATTGGGCAGAAGCTTGGTATCCACTCTGAAAGCTGCCATGG
GTGGATCCTTGGAGAGCATGGAGACTCAAGTGTTCCTGTGTGGAGTGGAGTGAATATCGCCGGCGTCCCTCTGAAGGATC
TGAACTCGGACATAGGAACTGATAAAGATCCCGAGCAGTGGAACAGTGTCCACAAAGATGTGATTGCCAGTGCGTATGAC
ATAATTAAGATGAAAGGTTATACTTCTTGGGCCATTGGCCTATCTGTAGCTGATTTATCAGAAAGCATTTTGAAGAATCT
CAAGAGAGTGCATCCAGTTTCCACCATAGTTAAGGGTCTCTATGGAATAAATGAAGAAGTATCCCTCAGTGTTCCTTGTG
TCCTGGGAGAGAATGGTATTACCGACCTTATAAAGGTGAAGCTGACTCCCGAAGAAGAGGCTCGTCTGAAGAAGAGTGCA
GAAACGCTTTGGAAGCTTCAGAAGGACTTAAAG

ORF - retro_pvam_1487 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.07 %
Parental protein coverage: 99.4 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMATLKEKLIAPVAEEAAVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSL
MAT.K..L......E..V..NKI...G.G.VGMACAISIL.K.L.DELALVD..EDK.KGE.MDLQHGS.
RetrocopyMATVKGELMSNLTSEEGVHRNKISIIGTGSVGMACAISILLKGLSDELALVDASEDKVKGETMDLQHGSP
ParentalFLQTPKIVADKDYSVTANSKVVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIIKYSPDCIIIVVSNPV
F...P.IV..KDY.VTANS.VVV.TAG.RQ..GE.RLNLVQRNV..FK.II..II.YSP.C..IVVSNPV
RetrocopyFMKMPNIVCSKDYLVTANSNVVVITAGARQEKGETRLNLVQRNVAIFKSIISNIIQYSPHCKLIVVSNPV
ParentalDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVA-VS
DILTYV.WKLS..P..RVIGSGCNLD.ARFR.L...KLGIH..SCHGWILGEHGDSSV.VWSGVN.A.V.
RetrocopyDILTYVAWKLSEFPQNRVIGSGCNLDTARFRFLIGQKLGIHSESCHGWILGEHGDSSVPVWSGVNIAGVP
ParentalLQELNPEMGTDNDSENWKEVHK-MVVSAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGM
L..LN...GTD.D.E.W..VHK....SAY..IK.KGYT.WAIGLSVADL.ES.LKNL.R.HPVST.VKG.
RetrocopyLKDLNSDIGTDKDPEQWNSVHKDVIASAYDIIKMKGYTSWAIGLSVADLSESILKNLKRVHPVSTIVKGL
ParentalYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLK
YGI..EV.LS.PC.L...G.T..I..KL...E.A.LKKSA.TLW..QKDLK
RetrocopyYGINEEVSLSVPCVLGENGITDLIKVKLTPEEEARLKKSAETLWKLQKDLK

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_1487 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 18 parental genes, and 56 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161754 retrocopies
retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Canis familiaris ENSCAFG000000121959 retrocopies
retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Cavia porcellus ENSCPOG000000071381 retrocopy
retro_cpor_762,
Dasypus novemcinctus ENSDNOG000000136204 retrocopies
retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Felis catus ENSFCAG000000126391 retrocopy
retro_fcat_462,
Gorilla gorilla ENSGGOG000000157581 retrocopy
retro_ggor_3033,
Loxodonta africana ENSLAFG000000009722 retrocopies
retro_lafr_197, retro_lafr_315,
Macropus eugenii ENSMEUG000000048251 retrocopy
retro_meug_311,
Microcebus murinus ENSMICG000000171832 retrocopies
retro_mmur_275, retro_mmur_300,
Myotis lucifugus ENSMLUG000000121551 retrocopy
retro_mluc_202,
Macaca mulatta ENSMMUG000000026794 retrocopies
retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica ENSMODG000000177861 retrocopy
retro_mdom_1484,
Mustela putorius furoENSMPUG000000001725 retrocopies
retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Mus musculus ENSMUSG000000302464 retrocopies
retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Otolemur garnettii ENSOGAG000000047639 retrocopies
retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pteropus vampyrus ENSPVAG00000002462 3 retrocopies
retro_pvam_1487 , retro_pvam_320, retro_pvam_673,
Rattus norvegicus ENSRNOG000000130003 retrocopies
retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
Sus scrofa ENSSSCG000000005761 retrocopy
retro_sscr_37,


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