RetrogeneDB ID: retro_pvam_127

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1531:57888..58490(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTPMT1
• Ensembl ID: ENSPVAG00000007341
• Aliases: None
• Description: protein tyrosine phosphatase, mitochondrial 1 [Source:HGNC Symbol;Acc:26965]

Sequence

>retro_pvam_127
ATGGCGGCCAGCGGGCTGCTGGAGGCCAGCCTGGCCTGAGTGCTCTTCTACCCAACATTGTTGTACATGCTGTTCTGTGG
GAAGATGCCAGGCCGGGCACATCACAACTAGTACCACCATAATGACCACACTATGTTGCTGGCCTCACTGCTGCTTCGAA
GCATGACTCACGGGCTGATACAGGATGAGAATGTGTGCAGGATGATCACCATGAACGAGTAGTATGAGATCAGGTCCCTG
TGCAACTCCTCAAAGGAGTGGAAGAGAGTAGGAGTTGAGCAGTTGTGACTCAGCACAGTAGAAATGACTGGAATCCCAAC
CTTGGCTAATCTCCAGAAAGGAGTCCAGTTTGCTCCCAAGTACCAGTTGCTGGGCCAGAGTGTCTATATGCACTATAAGG
CTGGGGGCTTCTGACTTACTGGGGGCTTCTGAAGTGTATCTGATTCAGGTGTACAACTGGAGTCCAGAGGAGGCTGTAAG
AGCCATCACCAAGATCCAGTCACACATCTACATCAGACCTGACCAGATGGAAATTCTCAATGAGTTTCACAGGGAGATTA
TTGCAAGGGCAGGAAAAGATAGGATGTCATACATCACAGACA

Alignment

ORF - retro_pvam_127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAGGLLEAGLARVLFYPTLLYTMFRGKVPGRAHRDWYHRIDHTVLLGALPLRSMTRRLIQDENVRGVIT
          MAA.GLLEA.LA.VLFYPTLLY..F.GK.PGRAH...YH..DHT.LL..L.LRSMT..LIQDENV...IT
Retrocopy MAASGLLEASLA*VLFYPTLLYMLFCGKMPGRAHHN*YHHNDHTMLLASLLLRSMTHGLIQDENVCRMIT

Parental  MNEEYETRFLCNSSKEWKRLGVEQLRLSTVDMTGIPTLANLQKGVQFVLKYQSLGQSVYVHCKA-GRSRS
          MNE.YE.R.LCNSSKEWKR.GVEQL.LSTV.MTGIPTLANLQKGVQF..KYQ.LGQSVY.H.KA.G.S..
Retrocopy MNE*YEIRSLCNSSKEWKRVGVEQL*LSTVEMTGIPTLANLQKGVQFAPKYQLLGQSVYMHYKA>GASDL

Parental  ATMVAAYLIQMYNWSPEEAVRAITKIRSHVYIRPGQMEILKEFHREIITGAAKDETS-TSQT
          ......YLIQ.YNWSPEEAVRAITKI.SH.YIRP.QMEIL.EFHREII..A.KD..S.TSQT
Retrocopy LGASEVYLIQVYNWSPEEAVRAITKIQSHIYIRPDQMEILNEFHREIIARAGKDRMS>TSQT

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_127 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	ENSPVAG00000007341	1 retrocopy	retro_pvam_127 ,
Sarcophilus harrisii	ENSSHAG00000017571	1 retrocopy	retro_shar_17,