RetrogeneDB ID:

retro_pvam_294

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_2385:339989..340493(-)
Located in intron of:ENSPVAG00000000170
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX3
Ensembl ID:ENSPVAG00000006297
Aliases:None
Description:chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]


Retrocopy-Parental alignment summary:






>retro_pvam_294
CAGAATAGAAAAAGTAGAAGAGTTGAAACAGCAGAGCCTGAAGAATTTGTGGTCGAAGAAGTACTAGACCAAAGCGTACT
GAATGGGAAAGTGGAGTACTTCCTAAAGTGGACGGGATTCACAGATGCCGACAATACTTGGGAACTGGAAGAAAATTTAG
ATAATCCAGAGTTAAGTGAAGCATTTCTTAATTCTCAAAAAGCTGGTAAAGAAAAAGATGGTACAAAAAGAGAAACTTTA
TCTGGCAATGAGTCTGATGATAGCAAATCAAAGAAGAAAAGAGATGCTGCTGATTAACCAAGAGGTTTTGCCAGAGGCCT
TGATCCTGAATGAGTAATTGGTGCCACAGACAACAATGGAGAATTAATGTTTCTCATAAAATGGAAAGATTACGATGAGG
CAGATTTGGTGCTGGCAAAAGAGACAAATATGAAATGTCTTCAAATTATAATTGCTTTTTATAAAGTGAGACTAACTTGG
CATTCTTGTCCAGAAAACAAAGCC

ORF - retro_pvam_294 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.14 %
Parental protein coverage: 96. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQKAGK
QN.KS..VE.AEPEEFVVE.VLD..V.NGKVEYFLKW.GFTDADNTWE.EENLD.PEL.EAFLNSQKAGK
RetrocopyQNRKSRRVETAEPEEFVVEEVLDQSVLNGKVEYFLKWTGFTDADNTWELEENLDNPELSEAFLNSQKAGK
ParentalEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAK
EKDGTKR..LS..ESDDSKSKKKRDAAD.PRGFARGLDPE..IGATD..GELMFL.KWKD.DEADLVLAK
RetrocopyEKDGTKRETLSGNESDDSKSKKKRDAAD*PRGFARGLDPE*VIGATDNNGELMFLIKWKDYDEADLVLAK
ParentalEANMKCPQIVIAFYEERLTWHSCPEDEA
E.NMKC.QI.IAFY..RLTWHSCPE..A
RetrocopyETNMKCLQIIIAFYKVRLTWHSCPENKA

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_294 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 11 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000289711 retrocopies
Callithrix jacchus ENSCJAG000000079528 retrocopies
Loxodonta africana ENSLAFG000000069073 retrocopies
Mus musculus ENSMUSG000000298361 retrocopy
Otolemur garnettii ENSOGAG000000165831 retrocopy
Ochotona princeps ENSOPRG000000117139 retrocopies
Pan troglodytes ENSPTRG0000001900310 retrocopies
Pteropus vampyrus ENSPVAG00000006297 2 retrocopies
retro_pvam_294 , retro_pvam_786,
Rattus norvegicus ENSRNOG000000118142 retrocopies
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
Sus scrofa ENSSSCG000000167114 retrocopies



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