RetrogeneDB ID: retro_pvam_275

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2294:371271..371732(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EXOSC8
• Ensembl ID: ENSPVAG00000014610
• Aliases: None
• Description: exosome component 8 [Source:HGNC Symbol;Acc:17035]

Sequence

>retro_pvam_275
CTACCACCTCTGTGTTCATCGAGATTTTGGTCTGCACCTCCTAGAGAAGAGGCTCGAGTAGCTGGTCAGTTCATTGTTGA
TGTCAATGAAAATTCACAGGTAATTCAAACAAGAGGACTTACGCATTTCTTCAGGAAAGCCTGCTTGGGTTCTATACTGT
GATCTTATTTGCCTCTGACTATGATGTAAATATTTTGAATGCTTGTACATTTGCTTTGTTAGGTGCTTTAAAAAAGTACA
GTTGTCTGAAATTACTATAAATGAAGAAATTGATTTAGCAGAAGTTAATTTAAAGAAAAAAAAGTTATTTGAACCTTAGA
ACTCATCCAGTTGTAACTTCCTTTGAGGTGTTTGATGACACTCTGCTCAGAGTTGACCCTACTGGAGAGAAGGAACACCT
AGCAACTGGAACTCTAACAGTGGTAATGGATGAGGAAGGCAAGCTACATTGTCTTCGCAAG

Alignment

ORF - retro_pvam_275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 55.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQ-KEDLCISPGKLAWVLYCDLICL-DYDGNILDAC
          LPPLCSSRF.S.PP.EEA.VA.QFI.DV.ENSQ.IQ..EDL.IS.GK.AWVLYCDLICL.DYD.NIL.AC
Retrocopy LPPLCSSRFWSAPPREEARVAGQFIVDVNENSQVIQ>QEDLRISSGKPAWVLYCDLICL>DYDVNILNAC

Parental  TFALLAAL-KNVQLPEVTINEETALAEVNLKKKSC-LNIRTHPVATSFAVFDDTLLIVDPTAEEEHLATG
          TFALL.AL.K.VQL.E.TINEE..LAEVNLK.....LN.RTHPV.TSF.VFDDTLL.VDPT.E.EHLATG
Retrocopy TFALLGAL<KKVQLSEITINEEIDLAEVNLKXXXL>LNLRTHPVVTSFEVFDDTLLRVDPTGEKEHLATG

Parental  TLTVVMDEESKLCCLHK
          TLTVVMDEE.KL.CL.K
Retrocopy TLTVVMDEEGKLHCLRK

Legend:

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

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_275 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000120699	1 retrocopy	retro_hsap_3585,
Gorilla gorilla	ENSGGOG00000011902	1 retrocopy	retro_ggor_2418,
Nomascus leucogenys	ENSNLEG00000001745	1 retrocopy	retro_nleu_1684,
Otolemur garnettii	ENSOGAG00000002745	2 retrocopies	retro_ogar_1154, retro_ogar_423,
Pongo abelii	ENSPPYG00000005287	1 retrocopy	retro_pabe_2071,
Pan troglodytes	ENSPTRG00000005790	1 retrocopy	retro_ptro_2429,
Pteropus vampyrus	ENSPVAG00000014610	1 retrocopy	retro_pvam_275 ,
Tupaia belangeri	ENSTBEG00000012040	9 retrocopies	retro_tbel_1492, retro_tbel_1680, retro_tbel_2932, retro_tbel_349, retro_tbel_3712, retro_tbel_4030, retro_tbel_419, retro_tbel_4649, retro_tbel_527,