RetrogeneDB ID: retro_pvam_1319

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_6095:26349..26789(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FHIT
• Ensembl ID: ENSPVAG00000016009
• Aliases: None
• Description: fragile histidine triad [Source:HGNC Symbol;Acc:3701]

Sequence

>retro_pvam_1319
GCATTCAGATTTGGCCAACAGCTCATCAGGCCCTTTGTGGTGGTTCTCAAAGAAGACCTGTCCTTTGCCCTCATGGACAG
GAAGCCTGAGTACCAGGACATGTACTCTCGTGTCCCCTGGGGCCAGTGGAGTACTTCTGAGACCTGCATCCTGTTGAAGC
GGCCAATTTGTTTCAAGCGACCCAAGGAGTCAGGACAATGGTGGGGAAGCATTTCAAGGAACTTCTCCTGCTTTTCTTCA
GGCAGGATGGCCTCAAAGTCAGACAGACTTTGATGAATGTTCACAGCCAGGTTCTTCCCAGGAAGGTGGGATATTTTCAC
AGGAATGACAGCGTCTATGATGAGCTCCATAAACGTGAAAAAGAGGAGCACTCTCCGATCTTGTGACAAAGAGAGGAGGG
AATGGCAGCAGAAGCTGCGGCACCGTGGGTTTCATTTCAG

Alignment

ORF - retro_pvam_1319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.09 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFRFGQHLIKPSVVFLKTELSFAFVNRKPV-VPGHVLVCPLRPVERFRDLHPNEVADLFQATQRVGTVVE
          .FRFGQ.LI.P.VV.LK..LSFA...RKP..VPGHVL.CPL.PVE.F.DLHP.E.A.LFQATQ.V.T.V.
Retrocopy AFRFGQQLIRPFVVVLKEDLSFALMDRKPE<VPGHVLSCPLGPVEYF*DLHPVEAANLFQATQGVRTMVG

Parental  KHFQGTSLTFAMQDGPEAGQTVKHVHIHVLPRKAGDFHRNDSIYDELQKHDKEEEDSPTLWRSEEEMAAE
          KHF....L.F..QDG....QT...VH..VLPRK.G.FHRNDS.YDEL.K..KEE..SP.L...EE.MAAE
Retrocopy KHFKELLLLFFRQDGLKVRQTLMNVHSQVLPRKVGYFHRNDSVYDELHKREKEEH-SPIL*QREEGMAAE

Parental  AAALRVCFQ
          AAA..V.FQ
Retrocopy AAAPWVSFQ

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_1319 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
Myotis lucifugus	ENSMLUG00000013987	1 retrocopy	retro_mluc_156,
Pteropus vampyrus	ENSPVAG00000016009	1 retrocopy	retro_pvam_1319 ,
Sorex araneus	ENSSARG00000008738	1 retrocopy	retro_sara_92,