RetrogeneDB ID: retro_pvam_27

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1015:675151..675736(-)
• Located in intron of: ENSPVAG00000008763

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIMP2
• Ensembl ID: ENSPVAG00000016092
• Aliases: None
• Description: aminoacyl tRNA synthetase complex-interacting multifunctional protein 2 [Source:HGNC Symbol;Acc:20609]

Sequence

>retro_pvam_27
ACATGTCCCTACAGAGGGCTCCCTTCACGCGCCTGGCTCCCCAGCGGCCCAGCAGGACTGGCAGCCCCATGCAGGGAGAG
TCTGACCCATCTCTTCGAGCTCTCGAGTCGCTGAGATGATGTTTTAAAACATCTGTATGAATTGAAAGCTGTGGTTGATG
GTCTTTCCAAGATGATTTGGGTGCGAGATGCGCACTTGCATGTAACCAACATAATCCAAGCCGATGAGCCCGCCGCTTTA
TTGCCCAATACACTGGACTTAAATTCATTGCTTGGGAAGGATTACAGGGTGCTGACAGACATCGTGATCATCGCAGACCC
CGCCTCCCCTCTTCTCTCCCTGCACCAGCTGTTCTGTGACCGCTCCTGGGTCCCGTTCACTGTCCACACACATTCAGCAG
TCAAGAGCGTGCCAGAAAACCTTGACTGCTTAAATTAGCAGACTAAAAAACAGTTCCTCGATGAATATCAGCTGGGTATT
ACTTTAATTTGGAAGAATGTGCCAAAGACTCGAATGAAGTTCAGTGTCCAAATGATGGGTCACATTAAAGGAGAAGGGAG
CATTGCATGTTTTTTGTTCTCTCTG

Alignment

ORF - retro_pvam_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64. %
• Parental protein coverage: 62.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TCMYR-LPNVHGGTSCPAPNAGHVQGESYPSLQTLESRQDDILKRLYELKAAVDGLSKMIQTPDADLDVT
          TC.YR.LP......S.PA..A.....ES...L..L.SR.DD.LK.LYELKA.VDGLSKMI...DA.L.VT
Retrocopy TCPYRGLPSRAWLPSGPAGLAAPCR-ESLTHLFELSSR*DDVLKHLYELKAVVDGLSKMIWVRDAHLHVT

Parental  NIIQASEPSALSTSALDLNSVLGKDYGALKDIVINANPASPPLSLLVLHRLLCDHFKVLSTVHTHSAVKN
          NIIQA.EP.AL....LDLNS.LGKDY..L.DIVI.A.PASP...LL.LH.L.CD...V..TVHTHSAVK.
Retrocopy NIIQADEPAALLPNTLDLNSLLGKDYRVLTDIVIIADPASP---LLSLHQLFCDRSWVPFTVHTHSAVKS

Parental  VPENLLKCFGEQTKNQSRHEYQLGFTLIWKNVPKTQMKFSVQRMCPIEGEGNIARFLFSL
          VPEN.L.C...QTK.Q...EYQLG.TLIWKNVPKT.MKFSVQ.M..I.GEG.IA.FLFSL
Retrocopy VPEN-LDCLN*QTKKQFLDEYQLGITLIWKNVPKTRMKFSVQMMGHIKGEGSIACFLFSL

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_27 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000016092	1 retrocopy	retro_pvam_27 ,
Rattus norvegicus	ENSRNOG00000001044	1 retrocopy	retro_rnor_2324,
Ictidomys tridecemlineatus	ENSSTOG00000029156	1 retrocopy	retro_itri_923,