RetrogeneDB ID: retro_pvam_854

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_1365:160340..160768(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IL18
• Ensembl ID: ENSPVAG00000014063
• Aliases: None
• Description: interleukin 18 (interferon-gamma-inducing factor) [Source:HGNC Symbol;Acc:5986]

Sequence

>retro_pvam_854
ATGGCTGCTGCATTATTAGAAGACAATTGCATCGGTTTTGTGGGAATAAACTTTATTGACAATACACTTTACTTTGTAAT
TGAAAGTGATGAAAACCTGGGAACAGATTACTTTGGCAAGCTTGAACCTCGGTTCTCAATCATATGAAATCTGAACAACC
AATTTCTCTTCATTTACGAGGAAAACCAAGCTGTGTTTAAAGATATGGCTGATTCTGACTGTATAGATAATGCATCCCAG
ACCAAATTTATATGTATGTATAAAGATAGCCTCACTAGAGGTCTGGCAGTAGCCATTTGTATGAAGTATAATAAAATTTT
TACTCTCTCGTAAGAACAAAATTATTCCTTTAAGGAAATTAATCCTCTTAATAATATCAATGATGAAGGAAATTACATCA
TATTTTTAAAAGAAGTGTTCTAGAACAT

Alignment

ORF - retro_pvam_854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.23 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAEPVEDDCISFVEMKFIDNTLYFVVKK-KNLESDYFGKLEPRFSIIRNLNNQVLFIYEGNTAVFEDMP
          MAA...ED.CI.FV...FIDNTLYFV.....NL..DYFGKLEPRFSII.NLNNQ.LFIYE.N.AVF.DM.
Retrocopy MAAALLEDNCIGFVGINFIDNTLYFVIESDENLGTDYFGKLEPRFSII*NLNNQFLFIYEENQAVFKDMA

Parental  DSDCTDNAPQTEFIIYMYKDSLTRGLAVAICVKCNKISTLSCDNKIISFKEMNPPDNINDDGNDIIF-FK
          DSDC.DNA.QT.FI..MYKDSLTRGLAVAIC.K.NKI.TLS......SFKE.NP..NIND.GN.IIF.FK
Retrocopy DSDCIDNASQTKFIC-MYKDSLTRGLAVAICMKYNKIFTLS*EQN-YSFKEINPLNNINDEGNYIIF<FK

Parental  RSVPEH
          RSV.EH
Retrocopy RSVLEH

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_854 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
Loxodonta africana	ENSLAFG00000028093	1 retrocopy	retro_lafr_425,
Mustela putorius furo	ENSMPUG00000003678	1 retrocopy	retro_mputfur_732,
Pteropus vampyrus	ENSPVAG00000014063	1 retrocopy	retro_pvam_854 ,