RetrogeneDB ID: retro_pvam_989

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_21213:7687..8181(+)
• 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_989
GCGCTGACAGATGGTGTGAGAATATTCAGCTTTGCCAGGAACGACAATGATTTTTATAGTTCACAAATACAAAGTGAAGA
AGCTCTAGAAAACATCTTTAAGTGACTATTCAATTTCTGATAACTATTATATTCCTGAAATAGCTAATATTTTGCTACTT
CAATCTTGTAAAATTTTAACCTACAAGATTGAACATGTATTTGGATTGCAACATTGTTAGGGGCTTGCATGCCTAATGCA
AGACTCCAATCATTTGGAATGAGCCAATAGCTGCCCTCTAAACCTTGGCCTGTCTATTTACTCAAGTTGCAGTGTGCTAT
TGGCTTCGACATATTGTAGAAAGATAAAGTGCTGGTGAGGTGGATTGATGATGAATCTGCTGATGCATCTGGAGTCAATC
TGAAACATATTCATGAGGATAATGTAATTTGCCAAAACTTGCGGAAACCTTTAAGGAATAGAAAAAGATAATAAAATTCC
TTGCAATGCTCCAA

Alignment

ORF - retro_pvam_989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.74 %
• Parental protein coverage: 65.37 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLTDGVGIFSFARYGNDFYSSH-YKGKVKTLQKKSSSDYSIFDNYYTPEVTSVLLLRSCKTLTHEIGHIF
          .LTDGV.IFSFAR..NDFYSS..YK..VK.L.K.S.SDYSI.DNYY.PE....LLL.SCK.LT..I.H.F
Retrocopy ALTDGVRIFSFARNDNDFYSSQ>YK--VKKL*KTSLSDYSISDNYYIPEIANILLLQSCKILTYKIEHVF

Parental  GVRHCQWLACLMQGSNHLEEADRRPLNL-CPICLRKLQCAIGFKIVERYKALVKWIDDESADTPGVTPKH
          G..HC..LACLMQ.SNHLE.A...PLNL..P..L.KLQCAIGF.I....K.LV.WIDDESAD..GV..KH
Retrocopy GLQHC*GLACLMQDSNHLE*ANSCPLNL<WPVYLLKLQCAIGFDIL*KDKVLVRWIDDESADASGVNLKH

Parental  SREDNV-NLPKPVEAFKEWREWIIKCLAVVQ
          ..EDNV.NLPK..E.FKE....IIK.LA..Q
Retrocopy IHEDNV<NLPKLAETFKE*KK-IIKFLAMLQ

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_989 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 ,