RetrogeneDB ID: retro_pvam_291

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2375:990775..991316(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JAM3
• Ensembl ID: ENSPVAG00000003230
• Aliases: None
• Description: junctional adhesion molecule 3 [Source:HGNC Symbol;Acc:15532]

Sequence

>retro_pvam_291
GGGCTGTGAAAGCTCAAATCCAGCAACCGAAACCCAATGGTATAGAATTTGAAAGTGTGGTGCTGTCTTGTATCATTACA
GATTTACAGGAAAATGACCCCACGATTGAATGAAAGAAAATTCAAGAAGCCAAACCACATATGTGTTTTTTTGAGAACAA
AATACAGGGAGATTTGTCAGGTCTGCAGAACTATTGGAGAAAACCTCTCTAAAGATCTGGAATGTGACCCAGACAGACTC
GGCCCTTTATCGCTGTGAGGTGGTTGCTCCAAAGGACCGCAAATAAATTAAGATTGTCCTGGAGTTAACCGTGCAAGTGA
GGCCAGTAGCTCCTGTGTGCCCACCAAACGTTGTGCCTGGAGGCAAGAAGGCAACGCTGCACTGCCAGGAGAGTGAGGAC
TACCCCGCGTCTCACATTTGGTGTTGCAATAATGTACCGCTGCCAAGAGACTTTAGCGCCAATCCAAAATTTCGAAATTC
TTTTCTTCTAAACGCTGAAATAGGCACTCTGGTTTGCAGCGCTGCTCACAGGGAGGGCAGT

Alignment

ORF - retro_pvam_291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.98 %
• Parental protein coverage: 52.26 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAVNLKSSNRNPVV-QEFESVELSCIITDSQTNDPRIEWKKIQDAQTTYVFFDNKIQGDLAG-RAELLGK
          G...LKSSNRNP.V..EFESV.LSCIITD.Q.NDP.IE.KKIQ.A.....FF.NKIQGDL.G..AELL.K
Retrocopy GL*KLKSSNRNPMV<IEFESVVLSCIITDLQENDPTIE*KKIQEAKPHMCFFENKIQGDLSG<SAELLEK

Parental  TSLKIWNVTRTDSALYRCEVVARNDRKAIDEIVIELTVQVKPVPPVCRVPKAVPVGKAATLHCQESEGYP
          TSLKIWNVT.TDSALYRCEVVA..DRK.I..IV.ELTVQV.PV.PVC..P..VP.GK.ATLHCQESE.YP
Retrocopy TSLKIWNVTQTDSALYRCEVVAPKDRK*I-KIVLELTVQVRPVAPVC-PPNVVPGGKKATLHCQESEDYP

Parental  PPHYSWYRNDVLLPTNSRANPRFRNSSFLLNSETGTLVFSAVHKEDS
          ..H..W..N.V.LP....ANP.FRN.SFLLN.E.GTLV.SA.H.E.S
Retrocopy ASHI-WCCNNVPLPRDFSANPKFRN-SFLLNAEIGTLVCSAAHREGS

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_291 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000003230	1 retrocopy	retro_pvam_291 ,