RetrogeneDB ID: retro_pvam_274

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2291:70692..71302(+)
• Located in intron of: ENSPVAG00000003887

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_274
TTGGCCTATGATGAAGTTATGGCTCAGCAGGATCAAATTCAGCATGAGATTGCTGCGTAGAACCCTCTGGTCTCAGAGCT
GCTGGAGCTCAGTCTTGAATAAGGAGTATGCCTGAGGATGGCATCCATCACCAGAAGATCAAGGACCTCCACAAAATGTA
CTCATACATCTGCAAGACCAGGCCTGATGGTAACTGCTGTTATTGAATCTTTGGATTCTCCCACTCAGAAGTGTTGCTGG
ATATCAGCAAGGAATTGCAGTGGTTCAAGGCTGTGTCTGCCAAGAGCAAAAAGGATCTGGTGTCACGGGGCTTCGTGAGT
TCACAGTTAAGGATTTCCACAACAATTTCATAGACCTAATTGAACAGGAAGAGAAGCAGACCTCAGTAGCTGGCCTGCTG
GCCTCCTTCTGTGACCAGAGGACCTTAGACTATCTGGTGGTCTATCTGCAACTGCTCGCCTCAGGCTTCTTGCATCATGA
CAGTGGTTCTTTAAATACTTCATCAAAGGTGGGCAAACTGTTAAGGAGTTCTGCCAGTAGGAAGTGGAGACCATGTACAA
ATAGAGTAATTACATCCACATTCATTGCATTGGCCCAGGCCCTCAATGTC

Alignment

ORF - retro_pvam_274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 82.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LAYDEAIMAQQDRIQQEIAVQNPLVSERLELSVL-YKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNCF
          LAYDE..MAQQD.IQ.EIA..NPLVSE.LELS........ED....Q..IKDLHK.YSYI.KTRPDGNC.
Retrocopy LAYDE-VMAQQDQIQHEIAA*NPLVSELLELSLE<IRSMPEDGIHHQK-IKDLHKMYSYICKTRPDGNCC

Parental  YRAFGFSHLEALLDDSKELQRFKAVSAKSKEDLVSQGFT-EFTIEDFHNTFMDLIEQVEKQTSVADLLAS
          Y..FGFSH.E.LLD.SKELQ.FKAVSAKSK.DLVS.GF..EFT..DFHN.F.DLIEQ.EKQTSVA.LLAS
Retrocopy Y*IFGFSHSEVLLDISKELQWFKAVSAKSKKDLVSRGFV<EFTVKDFHNNFIDLIEQEEKQTSVAGLLAS

Parental  FNDQSTSDYLVVYLRLLTSGYLQRESK-FFEHFIEGGRTVKEFCQQEVEPMCKESDHIHI-IALAQALSV
          F.DQ.T.DYLVVYL.LL.SG.L...S..FF..FI.GG.TVKEFCQ.EVE.M.K.S..IHI.IALAQAL.V
Retrocopy FCDQRTLDYLVVYLQLLASGFLHHDSG<FFKYFIKGGQTVKEFCQ*EVETMYK*SNYIHI>IALAQALNV

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_274 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,