RetrogeneDB ID: retro_pvam_1453

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_9051:43820..44404(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMZ2
• Ensembl ID: ENSPVAG00000017239
• Aliases: None
• Description: archaelysin family metallopeptidase 2 [Source:HGNC Symbol;Acc:28041]

Sequence

>retro_pvam_1453
GAAAGATATATTAAAGAGCTCAAGAGCTACTGTGAAGCATTTTGCTATGGCTTGACAGTAAAACTTCCAGAACAATTTCC
TGTTTCTGCAACTTAATATTCATTTAGATTCAATGACCACACATAAAACCTACAAATTCATATGGGGGGAATCCCTAAGT
TCATAAAAACAAAGAAACATGCAAATGTCTTCTGTATCATAAGTATAGCAATGATTGGTCTTTATCCAAGAGAGTCCTGG
AATTTTGTCTTTGAACAAGGCTCTTTGGTAGATGGCACAGAAATAGTCAGCTTTGCCAGATATGGCACTGGTTTTTATTT
TTATATTATGAGTACAACGCGAAAAAACTTGAGAAAATATCTTCAAGTGCCTATTCAGTTGTTAATAACTATTATTTTCC
TGAAATCACAAGTATTTTGCTACTTTGATCCCATAAGTGTTTAATCTATGAAATTGGACACAAGTTTGGACTCTGACACT
ACCACTGACTGGCAAGACTAATGCAAGGCTCTAGTCACCTGGAAAAACCAGACCATGGGCCTTTAGACCTTTGCCCCATC
TGCTTAAGTAAGTTACAGTGTGCT

Alignment

ORF - retro_pvam_1453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.24 %
• Parental protein coverage: 75.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEYIKWLKGYCEAFFYGLKVKLLEPIPVSATRCSFRVNDNTQNLQIHAGHILKFLKKRKPEDAFCVVGIT
          E.YIK.LK.YCEAF.YGL.VKL.E..PVSAT..SFR.ND.T.NLQIH.G.I.KF.K..K....FC...I.
Retrocopy ERYIKELKSYCEAFCYGLTVKLPEQFPVSAT*YSFRFNDHT*NLQIHMGGIPKFIKTKKHANVFCIISIA

Parental  MIDLYPRDSWNFVFGQASLTDGVGIFSFARYGNDFY-SSHYKGKVKTLQKKSSSDYSIFDNYYTPEVTSV
          MI.LYPR.SWNFVF.Q.SL.DG..I.SFARYG..FY....Y....K.L.K.SSS.YS...NYY.PE.TS.
Retrocopy MIGLYPRESWNFVFEQGSLVDGTEIVSFARYGTGFY<FLYYEYNAKKLEKISSSAYSVVNNYYFPEITSI

Parental  LLLRSCKTLTHEIGHIFGVRHCQWLACLMQGSNHLEEADRRPLNLCPICLRKLQCA
          LLL.S.K.L..EIGH.FG..H...LA.LMQGS.HLE..D..PL.LCPICL.KLQCA
Retrocopy LLL*SHKCLIYEIGHKFGL*HYH*LARLMQGSSHLEKPDHGPLDLCPICLSKLQCA

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_1453 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000493	1 retrocopy	retro_chof_2462,
Callithrix jacchus	ENSCJAG00000000254	1 retrocopy	retro_cjac_2798,
Cavia porcellus	ENSCPOG00000013061	1 retrocopy	retro_cpor_1226,
Pteropus vampyrus	ENSPVAG00000017239	2 retrocopies	retro_pvam_1453 , retro_pvam_989,