RetrogeneDB ID: retro_pvam_64

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1210:63751..64119(+)
• Located in intron of: ENSPVAG00000015224

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11B
• Ensembl ID: ENSPVAG00000009645
• Aliases: None
• Description: RAB11B, member RAS oncogene family [Source:HGNC Symbol;Acc:9761]

Sequence

>retro_pvam_64
ATGGGCACCCATGACGATGGGTGCGACTACCTCTTCGAAGTCGTCTGTATTGGAGATTCTGGTGTTGGAAAGAGTAATCT
GTCTCGATTTACTCAAAATGAGTTTGATCTCGAAAGCAAGAGCACCACTAGAGTAGATTTGCAACAAACAGCATCCAGAT
TGATGGGAAAACAATAAAGGCACAGATATGGGACACCCCAGGGCAAGAGCAATATCGAACTATAGTATCAGCATACTACT
GTGGAGCTGTAGGTGCCTTATTGGTTTATGACATTGCTAAATATCTCACACATGAAAATGTAGAGCGATGACTCAAAGAA
CCAAGAGATCATGCTGACAGTAACACTGTTATGCCTGTGGGCAACAAG

Alignment

ORF - retro_pvam_64 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 57.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVE-FATRSIQVDGKTIKAQIWDTAG
          MGT.DD..DYLF.VV.IGDSGVGKSNL.SRFT.NEF.LESKST..V..FAT.SIQ.DGKTIKAQIWDT.G
Retrocopy MGTHDDGCDYLFEVVCIGDSGVGKSNL-SRFTQNEFDLESKSTTRVD<FATNSIQIDGKTIKAQIWDTPG

Parental  QERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNK
          QE.YR.I.SAYY.GAVGALLVYDIAK.LT.ENVER.LKE.RDHADSN...M.VGNK
Retrocopy QEQYRTIVSAYYCGAVGALLVYDIAKYLTHENVER*LKEPRDHADSN-TVMPVGNK

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_64 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013525	1 retrocopy	retro_chof_1582,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866, retro_cjac_3917,
Erinaceus europaeus	ENSEEUG00000009165	2 retrocopies	retro_eeur_284, retro_eeur_565,
Mus musculus	ENSMUSG00000077450	1 retrocopy	retro_mmus_1846,
Otolemur garnettii	ENSOGAG00000003227	1 retrocopy	retro_ogar_2405,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pteropus vampyrus	ENSPVAG00000009645	1 retrocopy	retro_pvam_64 ,
Tupaia belangeri	ENSTBEG00000000667	1 retrocopy	retro_tbel_4634,