RetrogeneDB ID: retro_pvam_899

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_15662:13482..13915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPVAG00000017436
• Aliases: None
• Description: None

Sequence

>retro_pvam_899
ATGGCAGCTCAAATTCCAGTTGTGGCCACCATCACCACTCTGAGGATAGCCTGGAACAGCAAGAAGAGGCCAGCCAGTTC
TTCCCACAATGGCAACAGTGCTGGGGGATACAGCGCCAGTAAGAAGAAAAAAGCATCCACCTCTACTTTTGTGTAGGGTA
TCAGCATGAAAGCCATGACTGAGAATAAATGGTGCCTTCAGATTTTAGCACAGGACCTCTGGAAAAAACTGCCAAACCTT
TGACATTTAAAGATTCCAACTTTGTGCACTCTGGCCATGGTGGTGCAAGCAGAATAGAACCTGAAAGAACCTTAAACAAA
TTCTTGCTTCAGGAAGGGCATTGCCATGGCAACTGAATGATCCCAACTACTTCAGTATTGATGTTCCTCCATCCTTCAAT
CCAGCTAAGAAGTATTCTGATGTTTTAAATCTT

Alignment

ORF - retro_pvam_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.33 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAQIPIVATTTTPGIARNSKKRPASPSHNSSSAGIYSASKKKKASTSSFAQGISMEAMAENK-MVPSDF
          MAAQIP.VAT.TT..IA.NSKKRPAS.SHN..SAG.YSASKKKKASTS.F..GISM.AM.ENK.MVPSDF
Retrocopy MAAQIPVVATITTLRIAWNSKKRPASSSHNGNSAGGYSASKKKKASTSTFV*GISMKAMTENK<MVPSDF

Parental  STGPMEKTAKPLPFKDPNFVHSGHGGAVAGKKNRTWKNLKQILASE-RALPWQLNDPNYFSIDAPPSFKP
          STGP.EKTAKPL.FKD.NFVHSGHGGA......RT...L...L..E.RALPWQLNDPNYFSID.PPSF.P
Retrocopy STGPLEKTAKPLTFKDSNFVHSGHGGASRIEPERT---LNKFLLQE<RALPWQLNDPNYFSIDVPPSFNP

Parental  AKKYSDVSGL
          AKKYSDV..L
Retrocopy AKKYSDVLNL

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_899 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017884	1 retrocopy	retro_cfam_371,
Myotis lucifugus	ENSMLUG00000030708	3 retrocopies	retro_mluc_118, retro_mluc_1892, retro_mluc_1942,
Macaca mulatta	ENSMMUG00000020108	1 retrocopy	retro_mmul_1340,
Ochotona princeps	ENSOPRG00000011443	1 retrocopy	retro_opri_721,
Pteropus vampyrus	ENSPVAG00000017436	1 retrocopy	retro_pvam_899 ,