RetrogeneDB ID: retro_pvam_252

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2180:297185..297634(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL18
• Ensembl ID: ENSPVAG00000005322
• Aliases: None
• Description: mitochondrial ribosomal protein L18 [Source:HGNC Symbol;Acc:14477]

Sequence

>retro_pvam_252
TCAACCAGTTTCAAGCCAGAGGTGAAGCCCCAAGTGGACCTTTTAGAAAATAAAGCTGTTGCCCCAGAGTTCACCAGCCA
GAAAGCCTGGATCCTGGGGCTCTTAGCTGAAGCCAGGAAAGACTGGGGCTAGGAGACGGTGTGGGCCCCCCGCGAGTTCT
GGTACAGGTTCCGAGTTAAAAGGACTCAGCATCATATAGAAGCACTTGTTGATCACCGCAATGGCCAGGTTGCAGTTTCA
GCATCCATTCGTGAAAGGGCTATTAAAAAGCACCTTTATCGTACCAAAAATGTGATGGCTTGTGAGAGTATAGGGACCAT
TGCTGGCAAGAACGATGCTTCGAAGCAGGAAGCGACTTCATGGTCTACCAACCTAGTCCTTGGGAGGTGACCTCGGGCTC
GATGAAACGACTCTAGAGCACTATGACAGAAGATGCTACGGGGCTCGAG

Alignment

ORF - retro_pvam_252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.9 %
• Parental protein coverage: 82.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STSSKPEVKPEVDPLENEAIAPEFINRNPRNLELLALARKERGWGTVWPSREFWHRLRVIRTQHHIEAVV
          STS.KPEVKP.VD.LEN.A.APEF.......L.LLA.ARK..G..TVW..REFW.R.RV.RTQHHIEA.V
Retrocopy STSFKPEVKPQVDLLENKAVAPEFTSQKAWILGLLAEARKDWG*ETVWAPREFWYRFRVKRTQHHIEALV

Parental  EHRNGQVVVSASTREWAIKKYLYSTRNVVACESI-GRVLAG-RCLEAGINFMVYQPTPWEAASDSMQRLR
          .HRNGQV.VSAS.RE.AIKK.LY.T.NV.ACESI.G..LA..RC.EAG..FMVYQP.PWE..S.SM.RL.
Retrocopy DHRNGQVAVSASIRERAIKKHLYRTKNVMACESI>GPLLAR>RCFEAGSDFMVYQPSPWEVTSGSMKRL*

Parental  NAMTEGGVVLQ
          ..MTE....L.
Retrocopy STMTEDATGLE

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_252 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015398	1 retrocopy	retro_amel_1445,
Dipodomys ordii	ENSDORG00000011514	1 retrocopy	retro_dord_741,
Echinops telfairi	ENSETEG00000007591	1 retrocopy	retro_etel_438,
Homo sapiens	ENSG00000112110	1 retrocopy	retro_hsap_1664,
Gorilla gorilla	ENSGGOG00000014075	1 retrocopy	retro_ggor_1255,
Macaca mulatta	ENSMMUG00000017037	1 retrocopy	retro_mmul_61,
Mus musculus	ENSMUSG00000057388	1 retrocopy	retro_mmus_1940,
Otolemur garnettii	ENSOGAG00000007327	1 retrocopy	retro_ogar_1660,
Pongo abelii	ENSPPYG00000017147	3 retrocopies	retro_pabe_1416, retro_pabe_1418, retro_pabe_1421,
Pan troglodytes	ENSPTRG00000018761	1 retrocopy	retro_ptro_1128,
Pteropus vampyrus	ENSPVAG00000005322	2 retrocopies	retro_pvam_1480, retro_pvam_252 ,
Tarsius syrichta	ENSTSYG00000005598	1 retrocopy	retro_tsyr_1847,