RetrogeneDB ID:

retro_pvam_320

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_253:399159..399959(-)
Located in intron of:None
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_320
AAGGAAGAACAAAGCCCCCAGAATAAGATTATAGTCATTGGGGTTAGTGCTATTGGCATGGCCTATGTCATCAGTATCTT
ACTGAAAGACTTGGCAGATGAACTTGCCTCTGGTGGTGTCATGGAAGACAAATTGAATGGAGAGGTGATAGATCTCCAAA
ATGGCAGCCTTTTCCTTAGAACACCAAAAACTGTCTCTGGCAAAGACTATAAAGTGACTGCCAGCTCCAAGCTGGTTATT
ACCACCGCGAGGTACATCAACAAAAGGGAGAAAGCTGTCTTAATTTGGTCCAGCGTAAGGTGAATATCTTTAAATTCATC
ATTCCCAATGTTGTAAAATGCAGCCCTAACTGCAAATTGCTTATTGTTTCCAATTTAGTGGATATCTTGACCTATGTGGC
TTGGAAGATAAGCAGCTTTCCCCAAAGCCATGTTACCAGCAGTCGTTGCAATCTGGATTCATCCCAGTTCTGTTACTTCA
TAGGGGAAAGGCTAGGAATTCACCCATTAGGCTGTCATAGGTAGGTCTTTTGGGAGCATGGAGACTCTAATGTGCTTTGT
CTGGAGTGGAGTTAATGGTGCTGGTGTCTCCCTAAAGAATCTGCACCCTGATTTAGGCACTGATGCAGATGAGGAATGGT
GGAAATAAGTTCACAAACAGGTAGTTGACAGTGCTTATGAGTGATCAAATGGAGAGGTTACACGTCCTGGGCCATTGAAC
TATCTGTGGGAAACTTGGCGGAAAATATAATGAAGAACCTTGAGTGAATGCATTGAGTTTCCACCATGATTAAGGGACTC

ORF - retro_pvam_320 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.11 %
Parental protein coverage: 80.06 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEEAAVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDY
.E...P.NKI.V.GV...GMA..ISIL.K.LADELA...V.EDKL.GE..DLQ.GSLFL.TPK.V..KDY
RetrocopyKEEQSPQNKIIVIGVSAIGMAYVISILLKDLADELASGGVMEDKLNGEVIDLQNGSLFLRTPKTVSGKDY
ParentalSVTANSKVVVVTAG-VRQQEGESRLNLVQRNVNVFKFIIPQIIKYSPDCIIIVVSNPVDILTYVTWKLSG
.VTA.SK.V..TA..V.QQ.GES.LNLVQR.VN.FKFIIP...K.SP.C....VSN.VDILTYV.WK.S.
RetrocopyKVTASSKLVITTAR<VHQQKGESCLNLVQRKVNIFKFIIPNVVKCSPNCKLLIVSNLVDILTYVAWKISS
ParentalLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVA-VWSGVNVA-VSLQELNPEMGTD
.P...V..S.CNLDS..F.Y...E.LGIHP..CH.....EHGDS.V..VWSGVN.A.VSL..L.P..GTD
RetrocopyFPQSHVTSSRCNLDSSQFCYFIGERLGIHPLGCHR*VFWEHGDSNVL>VWSGVNGAGVSLKNLHPDLGTD
ParentalNDSENWKEVHKMVV-SAYE-VIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGM
.D.E.WK.VHK.VV.SAYE.VIK..GYT.WAI.LSV..L.E...KNL...H.VSTM.KG.
RetrocopyADEEWWK*VHKQVVDSAYE<VIKWRGYTSWAIELSVGNLAENIMKNLE*MH*VSTMIKGL

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






Pteropus vampyrus was not studied using RNA-Seq expression data.
Pteropus vampyrus was not studied using ChIP-Seq data.
Pteropus vampyrus was not studied using EST data.
Pteropus vampyrus was not studied using FANTOM5 data.
retro_pvam_320 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
Canis familiaris ENSCAFG000000121959 retrocopies
Cavia porcellus ENSCPOG000000071381 retrocopy
Dasypus novemcinctus ENSDNOG000000136204 retrocopies
Felis catus ENSFCAG000000126391 retrocopy
Gorilla gorilla ENSGGOG000000157581 retrocopy
Loxodonta africana ENSLAFG000000009722 retrocopies
Macropus eugenii ENSMEUG000000048251 retrocopy
Microcebus murinus ENSMICG000000171832 retrocopies
Myotis lucifugus ENSMLUG000000121551 retrocopy
Macaca mulatta ENSMMUG000000026794 retrocopies
Monodelphis domestica ENSMODG000000177861 retrocopy
Mustela putorius furoENSMPUG000000001725 retrocopies
Mus musculus ENSMUSG000000302464 retrocopies
Otolemur garnettii ENSOGAG000000047639 retrocopies
Pteropus vampyrus ENSPVAG00000002462 3 retrocopies
retro_pvam_1487, retro_pvam_320 , retro_pvam_673,
Rattus norvegicus ENSRNOG000000130003 retrocopies
Sus scrofa ENSSSCG000000005761 retrocopy



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