RetrogeneDB ID:

retro_pvam_116

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_1470:25320..25668(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGA1
Ensembl ID:ENSPVAG00000014283
Aliases:None
Description:high mobility group AT-hook 1 [Source:HGNC Symbol;Acc:5010]


Retrocopy-Parental alignment summary:






>retro_pvam_116
TCGAGCTCCAATTCCAGCCAACGCTTGGCCTCCAAGCAAAAAAGGACGGCACTGAGAAGCCAGGGCGGGGCAGGCCTCGC
AAGCCGCCTCGGGGGAGTCCTGGGGCGGCGCTGATAGGGAGTCGGAGAAAGCCCAGTGAAGTGCCAACACCGCAGAGACC
TCGGGCGACCCAAAGAGAGAAAAAACAACAGCGCTGCCAAGCCCAAAAACTAGAGGAGGAAGAAGAGGGCATCCCGCAGG
AGTCCTTAGAGGAGCAGTGACCGCGCAGTGCCACCTCACTGGGGGGCAGTTTCCTTCTGGAACTGGACGGCTCGGCTCCC
ACGGCCCCCGCCCCTTCCCATAGGCCCA

ORF - retro_pvam_116 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.39 %
Parental protein coverage: 65.48 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSSSKSSQPLASKQE-KDGTEKRGRGRPRKQPPVSPGTTLVGSQKEPSEVPTPKRPRGRPKGSK-NKGRRR
SSS.SSQ.LASKQ..KDGTEK.GRGRPRK.P..SPG..L.GS...PSEVPTP.RPR......K.N.....
RetrocopySSSNSSQRLASKQK<KDGTEKPGRGRPRKPPRGSPGAALIGSRRKPSEVPTPQRPRATQREKK>NSAAKP
ParentalKK-RASRRSPQR---RSSDRAVPP--ASSSRSSFLLGLDAPLPLPPCP
K..R...R...R...RSSDRAVPP.....S.......L..P.PLP..P
RetrocopyKN*RRKKRASRRSP*RSSDRAVPPHWGAVSFWNWTARLPRPPPLPIGP

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_116 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 7 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000152262 retrocopies
Macaca mulatta ENSMMUG000000195292 retrocopies
Mus musculus ENSMUSG000000467111 retrocopy
Procavia capensis ENSPCAG000000160761 retrocopy
Pongo abelii ENSPPYG000000298384 retrocopies
Pteropus vampyrus ENSPVAG00000014283 1 retrocopy
retro_pvam_116 ,
Rattus norvegicus ENSRNOG000000004881 retrocopy



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