RetrogeneDB ID: retro_pvam_67

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_122:114787..115413(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL1
• Ensembl ID: ENSPVAG00000002696
• Aliases: None
• Description: mitochondrial ribosomal protein L1 [Source:HGNC Symbol;Acc:14275]

Sequence

>retro_pvam_67
TCATATCCCTTTATGGAAGGTGAACCTGAGGATGATGTTTACTTAAAATGCCTATATCCAAGGCAGATATATGAGATGGA
GAAGCTCTTCACTTACTTAAGAAATTTCAAATTCTGGACCTTACAAATCCAAAGCAAGGTGTTTATCTTGATTTGACACT
GGATATGGCACTGAGAAAGAAGAAAAAAGTGGAACCATTTGCCAGTGTTCTTATTTTTCCATGCCAACTTGCTTCAGAAA
TCAATAAAGTTGCTGTATTTACAGGGAATGCATCAGAGATTAAAATAGCAGGAGAAAATGGAGCTGCATTTGTAGGAGGA
ACTAATCTGATCCGGAAGATTTTGGATGACGAAATTCAGTCAGACTATTATGTAGCTGTTCCATAAATAATGCCCGAGCT
TAATCCATTAAAGAAGAAACTGAAAAAAAAGATTTCCAAAGCTTACTCGAAATTCCATTGGCTGTGACATCCCCAAAATT
CTTGAATATTTAAAACTGGACATGAAATTAAAGTAGATGAAGAAAGGGAGAGTTTTCTTGAGACAAAAATAGCAACACTA
TATATGTCAAGTGACCAGATAGCTGCCAATTTGCAAGCAGTTAACAATGAAGTTTGTAGACACAGA

Alignment

ORF - retro_pvam_67 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 64.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SYPFMEGEPEDDVYLKRLYPRQIYEVKK-AIHLLKKFQILDFTNPKQGVYLDLTLDIALGKKKKVEPFAS
          SYPFMEGEPEDDVYLK.LYPRQIYE..K.A.HLLKKFQILD.TNPKQGVYLDLTLD.AL.KKKKVEPFAS
Retrocopy SYPFMEGEPEDDVYLKCLYPRQIYEMEK<ALHLLKKFQILDLTNPKQGVYLDLTLDMALRKKKKVEPFAS

Parental  VLSFPYPFTSEINKVAVFTGNASEIKIAEENGAAFAGGTNLIQKILDDEIQSDYYVAVPEIMPELNPLKK
          VL.FP....SEINKVAVFTGNASEIKIA.ENGAAF.GGTNLI.KILDDEIQSDYYVAVP.IMPELNPLKK
Retrocopy VLIFPCQLASEINKVAVFTGNASEIKIAGENGAAFVGGTNLIRKILDDEIQSDYYVAVP*IMPELNPLKK

Parental  KL-KKRFPKFTRNSIGRDIPKMLE-LFKTGHEIKVDEERENFLKTKIATLDMSSDQIAANLQAVINEVCR
          KL....FPK.TRNSIG.DIPK.LE..FKTGHEIKVDEERE.FL.TKIATL.MSSDQIAANLQAV.NEVCR
Retrocopy KL>XXXFPKLTRNSIGCDIPKILE<IFKTGHEIKVDEERESFLETKIATLYMSSDQIAANLQAVNNEVCR

Parental  HR
          HR
Retrocopy HR

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_67 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000024511	1 retrocopy	retro_ecab_665,
Myotis lucifugus	ENSMLUG00000011011	2 retrocopies	retro_mluc_2466, retro_mluc_534,
Pteropus vampyrus	ENSPVAG00000002696	2 retrocopies	retro_pvam_67 , retro_pvam_913,
Tursiops truncatus	ENSTTRG00000011899	1 retrocopy	retro_ttru_1405,