RetrogeneDB ID: retro_pvam_139

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1581:9572..9986(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL54
• Ensembl ID: ENSPVAG00000007137
• Aliases: None
• Description: mitochondrial ribosomal protein L54 [Source:HGNC Symbol;Acc:16685]

Sequence

>retro_pvam_139
ATGGCGGCCAAACACCTATTCGGGGCTACCTGGGCCTGGGAGGGCTGGCAGGCTCAGGAGCTCCTTGACCCCACTGTTCC
TGGAAGACTCCTTGGACAGGATTATGCCATGAAACTGGTCATTAAGAGTGGCAAAGGCAGCAAAGGCAGTGTGGTCAGTG
ATGCCCTGAAGGACCCAGAGGTGTGCACAGACTCCGTCCGGCTTACCACGTATGCCATAGGTGTCAACATCTACAAGGAG
TGCCAGGATGTGGTCCTGAAGTTGGAGGCCAAGCATCCTGAGTGGCTGTTTCAGATGAATGTGGGTCCCCCAGCAAAGAA
GCTAGAGGAACTGAACCATGAGACCTGGGAGTACTAGTGGCTGCTGCGGAAACATAACATCTGGTGCCACAATGGGCTGA
GCAAGAACCAAAAG

Alignment

ORF - retro_pvam_139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.42 %
• Parental protein coverage: 99.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAARHLFGATRTWAGWRVQQLPGPAASGRVFGRNYAKKPVIKD-KGSKGGVLSDALNDP-VCTDPVRLTT
          MAA.HLFGAT..W.GW..Q.L..P...GR..G..YA.K.VIK..KGSKG.V.SDAL.DP.VCTD.VRLTT
Retrocopy MAAKHLFGATWAWEGWQAQELLDPTVPGRLLGQDYAMKLVIKSGKGSKGSVVSDALKDPEVCTDSVRLTT

Parental  HAMGVNXXXXXXXXXXXXXXXXXXXLFQVNVGPP-KKLEELDPETREYWRLLRKHNIWRHNRLSKNRK
          .A.GVN...................LFQ.NVGPP.KKLEEL..ET.EY..LLRKHNIW.HN.LSKN.K
Retrocopy YAIGVNIYKECQDVVLKLEAKHPEWLFQMNVGPPAKKLEELNHETWEY*WLLRKHNIWCHNGLSKNQK

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_139 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000033519	1 retrocopy	retro_ogar_223,
Pteropus vampyrus	ENSPVAG00000007137	1 retrocopy	retro_pvam_139 ,
Rattus norvegicus	ENSRNOG00000020464	1 retrocopy	retro_rnor_1636,
Tupaia belangeri	ENSTBEG00000004745	1 retrocopy	retro_tbel_965,