RetrogeneDB ID: retro_pvam_539

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_365:125405..125835(-)
• Located in intron of: ENSPVAG00000000951

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5S
• Ensembl ID: ENSPVAG00000006173
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit s (factor B) [Source:HGNC Symbol;Acc:18799]

Sequence

>retro_pvam_539
AAGAAAGTGGATTATAAATGCATCTGGGATGTCAGCCCTGGCAGGGCAGCATCCAAGGGCTGCTGTGTTGTGGGGCCATA
GTGTGCTACCTTGCCCAGGAGAGGTAGCAGAAGGACTACAACAACTCCGCAACTAGCTCTCTGGATACATTTAAGATTAA
GGCGGTTGATGTCACTAGCTCTTCCATCATGAGCATTAGATTTGATTACATGGAGGACCTACAGCATGTTGAAAAAATAA
TGCTATGCAAATATCATAAATAAAAAAGGACTGTTAAGAGAGACTTGGTAAACTTGAAAATTTGCAGAAAAGCCTATTGG
AAATAATTTCACGTGGGAATATCACAGACAAGTCATCATTGCTTTTGTATTACTTAAGAAATCTTACATATTTGTTGTTC
AGTGATTTTCCTGAAATAAGAGAGAAAGGA

Alignment

ORF - retro_pvam_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.49 %
• Parental protein coverage: 55.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGVDYERIKDVGPDRAAS-EWLLRCGAMVRYHGQERWQKDYNNLPTGPLDKYKIQAIDATDSCIMSIGFD
          K.VDY..I.DV.P.RAAS...LL.CGA.V.Y..QER.QKDYNN..T..LD..KI.A.D.T.S.IMSI.FD
Retrocopy KKVDYKCIWDVSPGRAAS<QGLLCCGAIVCYLAQER*QKDYNNSATSSLDTFKIKAVDVTSSSIMSIRFD

Parental  HMEGLQHVEKIRLCKCHY-IEDHCLERLGQLENLQKSMLEMEIISCGNITDKGIIALHHLRKLKYLLLSD
          .ME.LQHVEKI.LCK.H..I...C.ERLG.LENLQKS.L..EIIS.GNITDK....L..LR.L.YLL.SD
Retrocopy YMEDLQHVEKIMLCKYHK<IKKDC*ERLGKLENLQKSLL--EIISRGNITDKSSLLLYYLRNLTYLLFSD

Parental  LPGTKNPG
          .P.....G
Retrocopy FPEIREKG

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_539 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009828	1 retrocopy	retro_amel_377,
Canis familiaris	ENSCAFG00000014285	1 retrocopy	retro_cfam_267,
Cavia porcellus	ENSCPOG00000014471	1 retrocopy	retro_cpor_740,
Felis catus	ENSFCAG00000029962	1 retrocopy	retro_fcat_72,
Loxodonta africana	ENSLAFG00000013773	1 retrocopy	retro_lafr_167,
Pteropus vampyrus	ENSPVAG00000006173	1 retrocopy	retro_pvam_539 ,
Sorex araneus	ENSSARG00000007707	1 retrocopy	retro_sara_694,