RetrogeneDB ID: retro_pvam_1017

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2273:117570..118029(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PYCR1
• Ensembl ID: ENSPVAG00000017874
• Aliases: None
• Description: pyrroline-5-carboxylate reductase 1 [Source:HGNC Symbol;Acc:9721]

Sequence

>retro_pvam_1017
AGCGTGGGCTTCATCGGCGCAGGGCAGCTAGCCTAGGCCCGGGCGCGGAGCTTCACAGCCGCAGGCATCCTGTCGGCTCA
CAAGATGATAGCCAGCTCTCCAGAAATGGACCTGTCTGCGGTGTCTGCGCTCAAGAAGATGAGGATGAACCTGACCCGGA
GCAACAATAAGATAGTGAGGAACAGCGACGTCCTGTTCCTGGCCATGAAGCTGCACATCATCCCCTTCATCCTGGACGGG
ATCGGTGCCGGTGTCCCGCCCAGGCACTTTGGAGTCTCTTGAACAGCCGGTGTCACCATCAGTTCAGTACAGAAGAAGCT
GACAGCGTTCCAGCCGGCCCCCAAGGTGATTCACTGCATGACCTACACACCTGTGCTGGTACAGGAGGGTGCCACAAGCA
CCCACGCCCTGGTGGAGGATGGGCAGCTCCTGGAGCAGTTCATGAGCAGCATGGGCTTT

Alignment

ORF - retro_pvam_1017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.15 %
• Parental protein coverage: 51.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVGFIGAGQLAFALAKGFTAAGVLTAHKIMASSPDMDLATVSSLRKMGVNLTSQNKETVQHSDILFLAVK
          SVGFIGAGQLA.A.A..FTAAG.L.AHK..ASSP.MDL..VS.L.KM..NLT..N...V..SD.LFLA.K
Retrocopy SVGFIGAGQLA*ARARSFTAAGILSAHKMIASSPEMDLSAVSALKKMRMNLTRSNNKIVRNSDVLFLAMK

Parental  PHIIPFILDEIGADIQDRHIVVSCAAGVTISSIEKKLTAFQPAPKVIRCMTNTPVVVREGATVYATGTHA
          .HIIPFILD.IGA....RH..VS..AGVTISS..KKLTAFQPAPKVI.CMT.TPV.V.EGAT.....THA
Retrocopy LHIIPFILDGIGAGVPPRHFGVS*TAGVTISSVQKKLTAFQPAPKVIHCMTYTPVLVQEGAT----STHA

Parental  QVEDSKLLEQLMSSVGF
          .VED..LLEQ.MSS.GF
Retrocopy LVEDGQLLEQFMSSMGF

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_1017 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	ENSPVAG00000017874	1 retrocopy	retro_pvam_1017 ,