RetrogeneDB ID: retro_pvam_913

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_16381:15942..16691(-)
• 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_913
TCACATCCCTTTATGGTAAGTGAACCTAAGGATGATGTTTACTTAAAACGCTTATATCCAAAACAGATATATGAGGTAGA
GAAAGCTATTCACTTAAGAAGTTTCAAATCCTGGACTTTACAAATCTAAAGCAAGGTATTTATCTTGATTTGACACTGGA
TATGGCACTGAGAAAGAAGAAAAAAGTGGAACCATTTGCCAGTGTTCTTATTTTTCCATGCCAACTTGCTTCAGAAATCA
ATAAAGTTGCTGTATTTACAGGGAATGCATCAGAGATTAAAATAGCAGGAGAAAATGGAGCTGCATTTGTAGGAGGAACT
AATCTGATCCGGAAGATTTTGGATGACGAAATTCAGTCAGACTATTATGTAGCTGTTCCATAAATAATGCCCGAGCTTAA
TCCATTAAAGAAGAAACTGAAAAAAAAGATTTCCAAAGTTTACTTGAAATTCCATTGGCCGTGACACCCCCAAAATGCTT
GAATTATTTAAAATTGGACATGAAGTTAAGGTAGATGAAGAAAGGAGGAATTTTCTTGAGACAAAAATAGCAACACTGGA
TATGTCAAATGACCAGATAACTGCCAATTTGCAAGCAGTTATCAGTGAAGTTTATAGGCACAGACCGCTGAATCTGGGAC
CCTTTGTGGTACAAGCTTTTCTTTGTAGGTTGACAAATGAAGGTTTGTTATTGAAGATAGAACTATTGTGCCCTAGAGAA
GTGAAACCAAAGAAAGCAACAAAGAAGCT

Alignment

ORF - retro_pvam_913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.1 %
• Parental protein coverage: 77.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SYPFMEGEPEDDVYLKRLYPRQIYEVKKAIHLLKKF-QILDFTNPKQGVYLDLTLDIALGKKKKVEPFAS
          S.PFM..EP.DDVYLKRLYP.QIYEV.KAIH.L..F.QILDFTN.KQG.YLDLTLD.AL.KKKKVEPFAS
Retrocopy SHPFMVSEPKDDVYLKRLYPKQIYEVEKAIH-LRSF<QILDFTNLKQGIYLDLTLDMALRKKKKVEPFAS

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

Parental  KL-KKRFPKFTRNSIGRDIPKMLELFKTGHEIKVDEERENFLKTKIATLDMSSDQIAANLQAVINEVCRH
          KL....FPKFT.NSIGRD.PKMLELFK.GHE.KVDEER.NFL.TKIATLDMS.DQI.ANLQAVI.EV.RH
Retrocopy KL>XXXFPKFT*NSIGRDTPKMLELFKIGHEVKVDEERRNFLETKIATLDMSNDQITANLQAVISEVYRH

Parental  RPLNLGPFVVRAFLRSSTSEGLLLKVEPLLPKEV-ETKESNQEA
          RPLNLGPFVV.AFL...T.EGLLLK.E.L.P.EV.ETKESN.EA
Retrocopy RPLNLGPFVVQAFLCRLTNEGLLLKIELLCPREV<ETKESNKEA

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_913 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,