RetrogeneDB ID: retro_pvam_135

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1559:411574..412161(+)
• Located in intron of: ENSPVAG00000001967

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN1
• Ensembl ID: ENSPVAG00000013681
• Aliases: None
• Description: tetraspanin 1 [Source:HGNC Symbol;Acc:20657]

Sequence

>retro_pvam_135
ATGCAGTGCTAGAGCTGTGCTAAGACCATGATGATCTTCTGAAATTTTCTTATCTTTCTGTGTGGTGCGGCCCTGCTGGC
AGTGGGCATCTGGGTGTCAGTCGATGGGCCATCCTTCCTAAAGATTTCTGGGCCACTGTCGTCCAGTGTCATGCAGTTTG
TCAATGTGGGCTATTTCCTCATTGCAACTGGTGCTGTGCTCTTTGCCCTTGGTTTCCTGAGCTGTTATGGTGCTCACACT
GAGAACAAGTGTGCCCTCATGATGTTCTTCTCCATCCTCCACCTCATCTTCACTGCTGAGGTTGCAGCTGCTGTGGTCGC
CCTGGTGTACGTAATGGCTGAGCGTTTCCTGACGTTGTTGGTAGTGCCCAGAAAGAAAGACTATCATTCTGAGAAGGACT
CCCCAGGTGTGGACACAAACCTAAAAGGGCTCAAGTGCTGTGGCTTCAAAAACTACATGGATTTGGAGGCTCTCTCCACC
TCTTATTAGAGAACCGTGTCTTTCCCCCATACTGCTGCTCTGATGATGCTGACAGCACAGCCAAGGAGCCTCGCGGCAAG
GAGAAGGCTGAGGACAAGGCTGCAGAG

Alignment

ORF - retro_pvam_135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.5 %
• Parental protein coverage: 82.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKCYSFVKNMMILFNFLIFLCGVALLAVGIWVSVDGSSFLKIFGPLSSSAMQFVNVGYFLIAAGALLFAL
          M.C.S..K.MMI..NFLIFLCG.ALLAVGIWVSVDG.SFLKI.GPLSSS.MQFVNVGYFLIA.GA.LFAL
Retrocopy MQC*SCAKTMMIF*NFLIFLCGAALLAVGIWVSVDGPSFLKISGPLSSSVMQFVNVGYFLIATGAVLFAL

Parental  GFLSCYGAHTENKCALMTFFLLLLIIFIAEVAAAVVALVYTAMGEHFLTMLVVPTIKKDYGSQSDFTQVW
          GFLSCYGAHTENKCALM.FF..L..IF.AEVAAAVVALVY..M.E.FLT.LVVP..KKDY.S..D...V.
Retrocopy GFLSCYGAHTENKCALMMFFSILHLIFTAEVAAAVVALVY-VMAERFLTLLVVPR-KKDYHSEKDSPGV-

Parental  NTTMKGLNCCGFNNYTDFE-GSPY-FLDNQVFPPYCCFDHVNDTVTEPCTKEKAENKAVQ
          .T..KGL.CCGF.NY.D.E.GS....L.N.VFPPYCC.D....T..EP..KEKAE.KA..
Retrocopy DTNLKGLKCCGFKNYMDLE<GSLHLLLENRVFPPYCCSDDADSTAKEPRGKEKAEDKAAE

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_135 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000004662	1 retrocopy	retro_pvam_394,
Pteropus vampyrus	ENSPVAG00000013681	1 retrocopy	retro_pvam_135 ,