RetrogeneDB ID: retro_pvam_1134

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_31624:3462..4108(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3M
• Ensembl ID: ENSPVAG00000015083
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit M [Source:HGNC Symbol;Acc:24460]

Sequence

>retro_pvam_1134
AGCATACGGGTCTTCGTTGTTATCAGTGAGGAAGATAAGGCTGCTGAGCTTTGAGCTTATCTAAAATCTACAGGAGTTGA
AATTTCAGAAGAGAACTCAGAAGGTGGACTTCATGTAAATTTAGCTCAAATTATTGAAGCTTGTGATGAATGTTTGAAGG
AAGACAATAAAGATATAGAAAGTGTGATGAACAGTATGGTATTCCTTCTACTAATCTTGGAATCAGATAATCAAGAAACT
CTGAAACCCTCTGTGAAAAGCTGGTCAAATTTTGGGAAGGTGAACATCGATCTCTGAGATTGCATTTGCTAAGCAACCTT
TTCTATGGGCTGGATAAGAATACTATTGTAAGATATACTGTGTATTGCAGCCTCATTAAAGTGGCAACATCTTGTGAGGC
CATACAGTATACTCCAATTAATCTAGATCGAGTTAGAAAATAGATTTCTGACTGGAACCTTACCACTGGAAAAAAAACCC
ACACTGTTTAAGGCTACTTTATGAGGTACATGTGGATTGTAAGAAAAGGGATGCCACTTCAAAAGTCATGGTCAAATTGC
TAGGAAGTTATATGGAGGACAATGCTTCCCAGGCTCTCATTGAAGCCAACGGGTATATTGTACCAGCATGGAAAGATCCA
AGTGCA

Alignment

ORF - retro_pvam_1134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.86 %
• Parental protein coverage: 58.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHIDLAQIIEACDVCLKEDDKDVESVMNSVVSLL
          S...F..ISEED.AAEL.AYLKS.G.EISEENSEGGLH..LAQIIEACD.CLKED.KD.ESVMNS.V..L
Retrocopy SIRVFVVISEEDKAAEL*AYLKSTGVEISEENSEGGLHVNLAQIIEACDECLKEDNKDIESVMNSMV-FL

Parental  LILEPEKQEALI-ENLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQYI
          L............E.LCEKLVKF.EGE..SLRL.LLSNLF.G.DKNT.VRYTVYCSLIKVA.SC.AIQY.
Retrocopy LLILESDNQETL<ETLCEKLVKFWEGEHRSLRLHLLSNLFYGLDKNTIVRYTVYCSLIKVATSCEAIQYT

Parental  PTELDQVRKWISDWNLNT-EKKHTL-LRLLYEALVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCI
          P..LD.VRK.ISDWNL.T....HT..LRLLYE..VDCKK.DA.SKVMV.LLGSY.EDNASQA...A...I
Retrocopy PINLDRVRK*ISDWNLTTXXXXHTV<LRLLYEVHVDCKKRDATSKVMVKLLGSYMEDNASQALIEANGYI

Parental  VRALKDPNA
          V.A.KDP.A
Retrocopy VPAWKDPSA

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_1134 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005338	2 retrocopies	retro_btau_1736, retro_btau_812,
Echinops telfairi	ENSETEG00000013437	1 retrocopy	retro_etel_120,
Myotis lucifugus	ENSMLUG00000014727	2 retrocopies	retro_mluc_1982, retro_mluc_431,
Mus musculus	ENSMUSG00000027170	1 retrocopy	retro_mmus_421,
Oryctolagus cuniculus	ENSOCUG00000004483	1 retrocopy	retro_ocun_282,
Otolemur garnettii	ENSOGAG00000015913	1 retrocopy	retro_ogar_1783,
Pteropus vampyrus	ENSPVAG00000015083	1 retrocopy	retro_pvam_1134 ,
Vicugna pacos	ENSVPAG00000007791	1 retrocopy	retro_vpac_342,