RetrogeneDB ID: retro_pvam_1214

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_42849:943..1396(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLP2
• Ensembl ID: ENSPVAG00000011770
• Aliases: None
• Description: proteolipid protein 2 (colonic epithelium-enriched) [Source:HGNC Symbol;Acc:9087]

Sequence

>retro_pvam_1214
ATGGAGGATTCCCAGCGTGACTCGGCCCCCAGCTACTGGGCCACCTGCACCAACTTCGCACGCAGCCAAAAGGGATTTCT
CCTGTTTGCTGAGATTATATTCTGCTTGGCAATTCTGTTGTGCTTCAGTGTCTCTGCACCAGTATATTCCTCCCTGTCTG
CGGGTCATATGACCGTTGCTGTTTTCTTCTTTGCCATCTACTCACTTAATCTGCACACCAAGATACACTGCATCAGCTGG
CCCTGGAGTGATTTCTTCCGAAGCTTTGTGACGGGGATCCTCTACTTGATATGATTTCCATTATTGTCCTTGATAAGAAA
GAAAATTGCTTCACTGTCGCTGCAGGGGTACTTGGCTAATCGTTACATGCCTCCTTTTCTATGATGCCTCTATCACTTCC
CGTGTGGTAGTAAAGACACAGCAGCCTATACTGATCTTGGAGATGGCCCGGTA

Alignment

ORF - retro_pvam_1214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADSERLSAPGCWAACTNLLRIRKGILLFAEIILCLVILICFSASTSAYSSLSVFEMILAAIFFVIYMCD
          M.DS.R.SAP..WA.CTN..R..KG.LLFAEII.CL.IL.CFS.S...YSSLS...M..A..FF.IY...
Retrocopy MEDSQRDSAPSYWATCTNFARSQKGFLLFAEIIFCLAILLCFSVSAPVYSSLSAGHMTVAVFFFAIYSLN

Parental  LNTKIKIINWPWSDFFRSLIAAILYLI-TSIVVLIERGHHSKIIA-GVLG-LIATCLFGFDAYDT-FPLK
          L.TKI..I.WPWSDFFRS....ILYLI.................A.GVLG.LI.TCL...DA..T.FP..
Retrocopy LHTKIHCISWPWSDFFRSFVTGILYLI<MISIIVLDKKENCFTVAAGVLG<LIVTCLLFYDASIT<FPC-

Parental  QQRHTAAPTDPADGPV
          ....TAA.TD..DGPV
Retrocopy GSKDTAAYTDLGDGPV

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_1214 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015798	1 retrocopy	retro_cfam_933,
Equus caballus	ENSECAG00000000216	1 retrocopy	retro_ecab_971,
Loxodonta africana	ENSLAFG00000004483	1 retrocopy	retro_lafr_427,
Mustela putorius furo	ENSMPUG00000013817	3 retrocopies	retro_mputfur_107, retro_mputfur_462, retro_mputfur_969,
Mus musculus	ENSMUSG00000031146	1 retrocopy	retro_mmus_94,
Pteropus vampyrus	ENSPVAG00000011770	2 retrocopies	retro_pvam_1214 , retro_pvam_810,
Pteropus vampyrus	ENSPVAG00000013762	1 retrocopy	retro_pvam_579,