RetrogeneDB ID: retro_pvam_1353

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_67537:4..915(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGED2
• Ensembl ID: ENSPVAG00000015485
• Aliases: None
• Description: melanoma antigen family D, 2 [Source:HGNC Symbol;Acc:16353]

Sequence

>retro_pvam_1353
AGGTGCCAAGAGCCTGAAGTGCCACCACCTTATGAGGTGGCCCTTTTGCTTTGGGAAAGCAAATGATTTAGTGAAGTATC
TGTTGGTTAAAGACCAGACAAAGATTCCCATTAAGCGCTCAGACATGCTGAAGGACATCATCAAAGAATACACTGATGTG
TACCCTGAAATTATTGAATGAGCAGGCTATTCCTTGGAGAAGGTATTTGGGATCCAACTGAAGGAAATCGATAAGAATGA
CCACCGTACATTCTTCTCAGCACCTTGGAGCCTACTGATGCAGGCATACTGGGAACAACCAAGGACTCTCCAAAGCTGGA
TCTTCTCATGGTGCTTCTTAGCATCATCTTCATGAATAGAAATCAGTCCAGTGAGGCTGTCATCTGGGAGATGCTGCACA
AGTTGGGGCTGCACCCCAGGATACTTCATTCGCTTTGGGGGGATGTGAAGAAGCTCATTACTGATGAGTTTCAACAGAAG
TCCCTGGACTATGCAAGAGTCCCTAATAGCAATCCCCCTGAGTATGAGTTCTTCTAGGGCCTGCATTCCTACTATAAGAG
CAACAAGATGAAAGTCCTCAAGTTTGCCTGCAAGGTACAAAAGAAGGATCCCAAGGAATGGGCAGCTCAGTACCGAGAGG
CAATGGAAGCAGATATGAAGCCTGTGGCTGAGGCTGCAGCTGAAGCCAAGGTGAGGGCCGAGATTAGAGCTCAAATGCAT
CTGGGCCTTGCAACTGAGATGAAGCTGATATTGGACCCTGGGCCAAAGCCCAGATCCAGGAAGGAGCTGAAGCTAAAGTC
AAAGCCCAAGAGAGTAGTGGTGCCAGTACTGGTGCTGATGTCAGTGGTGGCTTTGGTGCCAGTGCCAGCTTGACCCCCAC
TTCCATATTTGGGCTCTTCGCTGGCCTCAGT

Alignment

ORF - retro_pvam_1353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.3 %
• Parental protein coverage: 51.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RGQEPEVPPPYEVALLQ-GKANDLVKYLLVKDQTKIPIKRSDMLKDIIKEYTDVYPEIIERAGYSLEKVF
          R.QEPEVPPPYEVALL..GKANDLVKYLLVKDQTKIPIKRSDMLKDIIKEYTDVYPEIIE.AGYSLEKVF
Retrocopy RCQEPEVPPPYEVALLL>GKANDLVKYLLVKDQTKIPIKRSDMLKDIIKEYTDVYPEIIE*AGYSLEKVF

Parental  GIQLKEIDKNDHL-YILLSTLEPTDAGILGTTKDSPKLGLLMVLLSIIFMNGNRSSEAVIWEVLRKLGLR
          GIQLKEIDKNDH..YILLSTLEPTDAGILGTTKDSPKL.LLMVLLSIIFMN.N.SSEAVIWE.L.KLGL.
Retrocopy GIQLKEIDKNDHR<YILLSTLEPTDAGILGTTKDSPKLDLLMVLLSIIFMNRNQSSEAVIWEMLHKLGLH

Parental  PGIHHSLFGDVKKLITDEFVKQKYLDYARVPNSNPPEYEFFWGLRSYYETSKMKVLKFACKVQKKDPKEW
          P.I.HSL.GDVKKLITDEF..QK.LDYARVPNSNPPEYEFF.GL.SYY...KMKVLKFACKVQKKDPKEW
Retrocopy PRILHSLWGDVKKLITDEF-QQKSLDYARVPNSNPPEYEFF*GLHSYYKSNKMKVLKFACKVQKKDPKEW

Parental  AAQYREAMEADMKAAAEAAAEAKARAEIRARMGIGLGSE-NAAGPCNWDEADIGPWAKARIQA----GAE
          AAQYREAMEADMK..AEAAAEAK.RAEIRA.M..GL..E...A....W..A.I...A.A...A....GA.
Retrocopy AAQYREAMEADMKPVAEAAAEAKVRAEIRAQMHLGLATE<DEADIGPWAKAQIQEGAEAKVKAQESSGAS

Parental  AKAKAQESGGASNGANASGSFGASASLT
          ..A......GAS........FG..A.L.
Retrocopy TGADVSGGFGASASLTPTSIFGLFAGLS

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_1353 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000015485	1 retrocopy	retro_pvam_1353 ,