RetrogeneDB ID: retro_pvam_103

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1379:57980..58589(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LGALS3
• Ensembl ID: ENSPVAG00000016067
• Aliases: None
• Description: lectin, galactoside-binding, soluble, 3 [Source:HGNC Symbol;Acc:6563]

Sequence

>retro_pvam_103
GCTGGCACAGGGGGCTACCCAGGGGCCTCCTATCCTGGCAGCTGGCCCAGACCTGCACTTCCAGGAGCCTACTATATTTA
TCCTGGCCCAACAGCATCTGCTTAAGCTGGACCAATTGCACCAGGAGCCTACCCCAGGCAACCAGGGGGCCCTGGGGCCT
ACCCTGGTGCCAGCCCCATTGACGTCCATACTAGACCACTGACTGTGCCTTATGACCTGGCTTTTCCTGGAGGAGCGATG
CCTCACATGCTGATAACAATTCTGGGCACAGTAAAGCCCAATGCAAACAGACTTGTTTTAGATTTCAAGAAAGGGAATGA
TGTCGCCTTTCACTTTAACCCACGCTTCAGTGAGGACAACAGGAGAGTCATTGTTTGCAATCCAAAGCTGAATAATACCT
GGGGACCAGAAGAAAGAGAGATAGTTTTCCCATTTGAAAGTGGTAAACCATTCAAAATACAAGCACCAGTTGAATCTGAC
CACTTCAAGTTTGCAGTCAATGATGCTCACTTGTTGCAGTACAATCATCGGGTGAAAAATCTCAAGAAAATCAGCATGGT
GGGAATTTCCTGTGATGTCAATCTCACCAAGGCATACTATGATATAATC

Alignment

ORF - retro_pvam_103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.88 %
• Parental protein coverage: 79.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APPGAYPGQAPPGAYPGQA-PPGAYPGQAPPGAYPGLPCGPTACLSSGQPGGPGAYPGAGPTGTPAGPLT
          A..G.YPG...PG..P..A.P...Y....P.......P..P.A.....QPGGPGAYPGA.P......PLT
Retrocopy AGTGGYPGASYPGSWPRPALPGAYYIYPGPTASA*AGPIAPGAY--PRQPGGPGAYPGASPIDVHTRPLT

Parental  VP-DLAFPGGVMPRMLITILGTVK-NANKITLDFKRGNDIAFHFNPRFNENNRRVIVCNSKMNNNWGPEE
          VP.DLAFPGG.MP.MLITILGTVK.NAN...LDFK.GND.AFHFNPRF.E.NRRVIVCN.K.NN.WGPEE
Retrocopy VPYDLAFPGGAMPHMLITILGTVKPNANRLVLDFKKGNDVAFHFNPRFSEDNRRVIVCNPKLNNTWGPEE

Parental  RQMVFPFESGKPFKIQVLVEDDHFKVAVNDAHLLQYNHRMKNLKEISAVGIAGDVTLISASHAMI
          R..VFPFESGKPFKIQ..VE.DHFK.AVNDAHLLQYNHR.KNLK.IS.VGI..DV.L..A....I
Retrocopy REIVFPFESGKPFKIQAPVESDHFKFAVNDAHLLQYNHRVKNLKKISMVGISCDVNLTKAYYDII

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_103 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015013	1 retrocopy	retro_cfam_2018,
Mustela putorius furo	ENSMPUG00000005725	2 retrocopies	retro_mputfur_115, retro_mputfur_535,
Pteropus vampyrus	ENSPVAG00000016067	1 retrocopy	retro_pvam_103 ,
Tarsius syrichta	ENSTSYG00000009020	4 retrocopies	retro_tsyr_1233, retro_tsyr_1390, retro_tsyr_1784, retro_tsyr_625,