RetrogeneDB ID: retro_pvam_222

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1981:250925..251336(-)
• Located in intron of: ENSPVAG00000007424

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA5
• Ensembl ID: ENSPVAG00000008908
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 5 [Source:HGNC Symbol;Acc:9534]

Sequence

>retro_pvam_222
GAGTATGGCAGGGGTATGAATACTTGTTCTCCTGAAGGAAGATGATTTCAAGTGGAATGTGCAATTGAGGCTATCAAGCT
TGGTTCTACAGTTACTGGAATCCAGATACTGGAGGGTGTGTGCTCAGCTATGGGGAAGAGAATTATCTCCCCACTCATGG
AGCCAGGCAGCACTGAGAGAATTGTAAAGACTGATGCTCAGATAGGTTATGCCATGAGTGAGCCTACTGCTGATGCTAAG
ATTTTAATTGATAAAGCCAGAGTGGAGACACAGAATCACTGGTCCACCTACAATGAGACAATGACAGTGGAAGGTGTAAT
CCAGGCTGTGTCCAATCTGGCTCTACGGTTTGGAGAAGAAGATGCAGATCTGGGTGCCATGTCTTGTCTATTTGGAGTAG
CACTGTTATTT

Alignment

ORF - retro_pvam_222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.37 %
• Parental protein coverage: 56.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGC
          EY.RG.NT.SPEGR.FQVE.AIEAIKLGST..GIQ..EGVC.A..KRI.SPLMEP.S.E.IV..DA.IG.
Retrocopy EYGRGMNTCSPEGR*FQVECAIEAIKLGSTVTGIQILEGVCSAMGKRIISPLMEPGSTERIVKTDAQIGY

Parental  AMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLF
          AMS...ADAK.LIDKARVETQNHW.TYNETMTVE.V.QAVSNLAL.FGEEDAD.GAMS..FGVALLF
Retrocopy AMSEPTADAKILIDKARVETQNHWSTYNETMTVEGVIQAVSNLALRFGEEDADLGAMSCLFGVALLF

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_222 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008497	2 retrocopies	retro_mluc_1002, retro_mluc_926,
Mustela putorius furo	ENSMPUG00000003189	1 retrocopy	retro_mputfur_1295,
Mus musculus	ENSMUSG00000068749	1 retrocopy	retro_mmus_52,
Otolemur garnettii	ENSOGAG00000013560	1 retrocopy	retro_ogar_3137,
Pteropus vampyrus	ENSPVAG00000008908	1 retrocopy	retro_pvam_222 ,
Sus scrofa	ENSSSCG00000006830	2 retrocopies	retro_sscr_1156, retro_sscr_1194,