RetrogeneDB ID: retro_pvam_131

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1551:8068..8527(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTUB1
• Ensembl ID: ENSPVAG00000017099
• Aliases: None
• Description: OTU domain, ubiquitin aldehyde binding 1 [Source:HGNC Symbol;Acc:23077]

Sequence

>retro_pvam_131
CTGTCTGCCAAGATTAAAGAGGACCTGGTGTTCCAGCGCTTCACCAAGTTCACAATTAAAGATTTCCACAACATATTCAC
AGACCTGATTGAGCAGGTAAAGAAGCAGACCTCAGTAGCCTATCTGCTGGCCTCCTTCAATGACCAGAGCACCTGCAACT
ACCTGGTAGTTTACCAGCAGCTGCTCACTTCAGGCCACCTGCAGCATAACAGCAAGTTTTCTGAGTACTACATCAAGGGT
GTGTGAACTGTCAAGGAGTTCTGCCATCAGGAGGTGGAGCCCATGTGCAAGGAGACTGATCACATCTACGTTATCACGCT
GGCCCAGGCCTTCAGTGTCTCCATCCAGATGGAGGACATAGACCATGGTGAAGACAACACCACCAGTCGGCACATTTCCT
CTGAGGGCTCTGAGCCAAAGGTCTACCTTCTCAGCTGGCCTGGACACTACAGTATCCTA

Alignment

ORF - retro_pvam_131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.55 %
• Parental protein coverage: 60.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQVEKQTSVADLLASFNDQSTSDYLVVYLRLLTSGYLQRE
          .SAK.KEDLV.Q.FT.FTI.DFHN.F.DLIEQV.KQTSVA.LLASFNDQST..YLVVY..LLTSG.LQ..
Retrocopy LSAKIKEDLVFQRFTKFTIKDFHNIFTDLIEQVKKQTSVAYLLASFNDQSTCNYLVVYQQLLTSGHLQHN

Parental  SKFFEHFIEGGRTVKEFCQQEVEPMCKESDHIHIIALAQALSVSIQVEYMDRGEGGTTNPHIFPEGSEPK
          SKF.E..I.G..TVKEFC.QEVEPMCKE.DHI..I.LAQA.SVSIQ.E..D.GE..TT..HI..EGSEPK
Retrocopy SKFSEYYIKGV*TVKEFCHQEVEPMCKETDHIYVITLAQAFSVSIQMEDIDHGEDNTTSRHISSEGSEPK

Parental  VYLLYRPGHYDIL
          VYLL..PGHY.IL
Retrocopy VYLLSWPGHYSIL

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_131 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018084	1 retrocopy	retro_amel_1270,
Bos taurus	ENSBTAG00000003967	1 retrocopy	retro_btau_1119,
Canis familiaris	ENSCAFG00000014729	2 retrocopies	retro_cfam_1376, retro_cfam_2023,
Equus caballus	ENSECAG00000002621	1 retrocopy	retro_ecab_760,
Myotis lucifugus	ENSMLUG00000012235	2 retrocopies	retro_mluc_1257, retro_mluc_614,
Mustela putorius furo	ENSMPUG00000013314	1 retrocopy	retro_mputfur_1057,
Pteropus vampyrus	ENSPVAG00000017099	2 retrocopies	retro_pvam_131 , retro_pvam_274,
Rattus norvegicus	ENSRNOG00000021175	1 retrocopy	retro_rnor_2431,
Sarcophilus harrisii	ENSSHAG00000004156	1 retrocopy	retro_shar_87,