RetrogeneDB ID: retro_pvam_591

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3950:425562..426298(-)
• Located in intron of: ENSPVAG00000013040

Retrocopy information

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

Parental gene information

• Parental gene symbol: CERS5
• Ensembl ID: ENSPVAG00000006713
• Aliases: None
• Description: ceramide synthase 5 [Source:HGNC Symbol;Acc:23749]

Sequence

>retro_pvam_591
AAAAATCCATTGCTTAGTAAATTCTGTGAAAGCATTTGGAGATTCACTTTTTATTTATGTATATTTTGCTGTGGAATTAG
ATTTCTGTGGTCATCACCTTGGTTTTGGGACACCCGACACTGCCGGCATGGCTGTCTTATCAGCCTCTCAGAAGTGGGCT
TTATTACTATTATATCATGGAACTGGCCTTCTGTTGGTCTCATGTTTTCTCAGTTTACAGACATTAAAAGAAAGGACTTT
CTGATCATGTTTGTGCATCACTCGGCCACCATTGGGCTCATCACCTTCTCCTACATCAGGAACATGGTCTGGGTAGGAAC
TCTGGTCATGTGTCTACATGATGCTTCAGATTTCTTGCTAGAAGCAGCCAAGCTGGTCAGTTATGCCAGGTATCAGTGTC
TCTGTGACACCCTTTTTGTGATCATCAGTGCTGTTTTTATGGTCACTCATCTAGGAATCTCTCCATTCGGAATTCTGAAC
ATGACTCTCTTTGAGAGTTGGGAGGTAATTGGGCCCTGTCCCTCCTGGTGGCTCTTCAGTGGCATTCTCCTAATCCTGTA
GGTTCTGCATGTCATCTGGTCCTACCTAATTGTGTGAATTGCTTTCAAAGCTTTGATCCAAGGAAAGGTGTCTAAGATTG
GTTGCAGTGTTGTGGAGAGCAGCTCAGAAGAAGATGTGACCACCAACACAAAAGACCCTGTGGCAGCAACTCCAGCAATG
CGCCAATTGGGTGAAT

Alignment

ORF - retro_pvam_591 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.28 %
• Parental protein coverage: 65.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KPPTLTKFCESMWRFTFYLCIFCYGIRFLWSSPWFWDTRQCWHS-YPYQPLTSGLYNYYIMELAFYWSLM
          K.P.L.KFCES.WRFTFYLCIFC.GIRFLWSSPWFWDTR.C.H....YQPL.SGLY.YYIMELAF.WS..
Retrocopy KNPLLSKFCESIWRFTFYLCIFCCGIRFLWSSPWFWDTRHCRHG<LSYQPLRSGLYYYYIMELAFCWSHV

Parental  FSQF-TDIKRKDF-LIMFVHHLATIGLITFSYINNMVRVGTLVMFLHDSSDFLLEAAKLANYAKYQRLCD
          FS......K...F.LIMFVHH.ATIGLITFSYI.NMV.VGTLVM.LHD.SDFLLEAAKL..YA.YQ.LCD
Retrocopy FSVY<QTLKERTF<LIMFVHHSATIGLITFSYIRNMVWVGTLVMCLHDASDFLLEAAKLVSYARYQCLCD

Parental  TLFVIFSAVFMVTRLVIYPFWILNTTLFESWEMIGPYPSWWLFNGLLLILQVLHVIWSYLIARIAFKALI
          TLFVI.SAVFMVT.L.I.PF.ILN.TLFESWE.IGP.PSWWLF.G.LLIL.VLHVIWSYLI..IAFKALI
Retrocopy TLFVIISAVFMVTHLGISPFGILNMTLFESWEVIGPCPSWWLFSGILLIL*VLHVIWSYLIV*IAFKALI

Parental  RGKVSKDDRSDVESSSEEDDVTTYT-KRPCDSSSSNG-ANWVN
          .GKVSK...S.VESSSEE.DVTT.T.KRPC.S.SSN..ANWVN
Retrocopy QGKVSKIGCSVVESSSEE-DVTTNT<KRPCGSNSSNA<ANWVN

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_591 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000012843	1 retrocopy	retro_ocun_1643,
Otolemur garnettii	ENSOGAG00000004668	1 retrocopy	retro_ogar_392,
Pteropus vampyrus	ENSPVAG00000006713	1 retrocopy	retro_pvam_591 ,
Sus scrofa	ENSSSCG00000024932	1 retrocopy	retro_sscr_1195,