RetrogeneDB ID: retro_pvam_1354

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_67909:79..549(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB8A
• Ensembl ID: ENSPVAG00000009756
• Aliases: None
• Description: RAB8A, member RAS oncogene family [Source:HGNC Symbol;Acc:7007]

Sequence

>retro_pvam_1354
ATGTTCAATCAGCTGCTGAACGGGGACTTGGGGGTGGGGAAGATCTAGTCTTGTTCCACTTCTCCGAGGACACCTTCAAC
TCCATTTTCATTTCCATCATAGGAATTGACTTTATAGCCAGGACCATAGAGCTCAATGGCAAGAGATTTAAACTACAGAT
ATGGGACACAGCTGGCCAGGAATAGTGTCGATGGTCATAACAGCCTACTACGGGGGTGCAAAGGGCATCACTCTGGTCTG
TGACATCACCAATGAGAAGTCCTTTTACAAGAGCCAAATTGGATTCTGAACATTGAGGAGCATGCTTCTGTAGATGTCAA
AAAGATGATACTTGGGAACAAGTGCGACATGAATAACGAGAGAGAAGTGTCCAAAGAACGGGGAGAAAGCTGGCCCTGGA
CTATGGAATTAAGTTCATGGAGACCAGCACCAAGGCCAACATCAATATGAAGAATGCATTTTTCACTCTC

Alignment

ORF - retro_pvam_1354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 76.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LFKLLLIGDSGVGKT-CVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGQERFR-TITT
          .F..LL.GD.GVGK...VLF.FSED.FNS.FIS.IGIDF..RTIEL.GKR.KLQIWDTAGQE..R....T
Retrocopy MFNQLLNGDLGVGKI<LVLFHFSEDTFNSIFISIIGIDFIARTIELNGKRFKLQIWDTAGQE*CR<MVIT

Parental  AYYRGAMGIMLVYDITNEKSFDNIR-NWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGE-KLALDY
          AYY.GA.GI.LV.DITNEKSF.....NWI.NIEEHAS.DV.KMILGNKCD.N..R.VSKERGE.KLALDY
Retrocopy AYYGGAKGITLVCDITNEKSFYKSQ<NWILNIEEHASVDVKKMILGNKCDMNNEREVSKERGE<KLALDY

Parental  GIKFMETSAKANINVENAFFTL
          GIKFMETS.KANIN..NAFFTL
Retrocopy GIKFMETSTKANINMKNAFFTL

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_1354 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014120	1 retrocopy	retro_cjac_1494,
Otolemur garnettii	ENSOGAG00000013894	1 retrocopy	retro_ogar_2356,
Pteropus vampyrus	ENSPVAG00000009756	1 retrocopy	retro_pvam_1354 ,