RetrogeneDB ID: retro_pvam_65

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1216:50482..50790(+)
• Located in intron of: ENSPVAG00000017761

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL31
• Ensembl ID: ENSPVAG00000011716
• Aliases: None
• Description: ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]

Sequence

>retro_pvam_65
ATAGCTCCCACAAGGAAGAGTGGTGAGAGAAGAAAGGGCCACGCTGCCAACAGTGAGGTGGCGACCAGAGAGAACCCCAC
CAACATTGGCAAGTGCATCCACAGAATGAGCTTCCAGAGAGGTTCCTCTTAGGCATTCAAAGAGATGCAGAAATTTCCCA
GGAAAGAGACAGGAACTCCAGATGTGCACATGGACTCCAGGCTCAACAAAGCTACTGGGCCAAAGGAATAAGGACTGTTC
CATACCTTATCAGTATATGGTTGCCCAGAAAGTATAATGAAGATGAAGATTTGCCAAAGTCTATACAT

Alignment

ORF - retro_pvam_65 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.88 %
• Parental protein coverage: 82.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPAKKGSEKKKGRSAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNK
          .AP..K..E..KG..A..EV.TRE...NI.K.IH...F......A.KE..KF..KE.GTPDV..D.RLNK
Retrocopy IAPTRKSGERRKGHAANSEVATRENPTNIGKCIHRMSFQRGSS*AFKEMQKFPRKETGTPDVHMDSRLNK

Parental  AV-WAKGIRNVPYRIRVRLSRKRNEDEDSPNKLY
          A..WAKGIR.VPY.I...L.RK.NEDED.P....
Retrocopy AT<WAKGIRTVPYLISIWLPRKYNEDEDLPKSIH

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_65 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 9 parental genes, and 83 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Loxodonta africana	ENSLAFG00000027873	12 retrocopies	retro_lafr_118, retro_lafr_187, retro_lafr_20, retro_lafr_245, retro_lafr_307, retro_lafr_56, retro_lafr_663, retro_lafr_703, retro_lafr_710, retro_lafr_778, retro_lafr_885, retro_lafr_926,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Otolemur garnettii	ENSOGAG00000014494	10 retrocopies	retro_ogar_103, retro_ogar_143, retro_ogar_150, retro_ogar_178, retro_ogar_181, retro_ogar_186, retro_ogar_262, retro_ogar_271, retro_ogar_29, retro_ogar_3,
Pongo abelii	ENSPPYG00000025870	4 retrocopies	retro_pabe_106, retro_pabe_1635, retro_pabe_168, retro_pabe_895,
Pteropus vampyrus	ENSPVAG00000011716	17 retrocopies	retro_pvam_1131, retro_pvam_1265, retro_pvam_1359, retro_pvam_197, retro_pvam_349, retro_pvam_410, retro_pvam_441, retro_pvam_469, retro_pvam_484, retro_pvam_501, retro_pvam_565, retro_pvam_606, retro_pvam_631, retro_pvam_65 , retro_pvam_815, retro_pvam_861, retro_pvam_864,
Sus scrofa	ENSSSCG00000008170	4 retrocopies	retro_sscr_1072, retro_sscr_1073, retro_sscr_128, retro_sscr_263,
Sus scrofa	ENSSSCG00000025180	6 retrocopies	retro_sscr_20, retro_sscr_34, retro_sscr_469, retro_sscr_501, retro_sscr_713, retro_sscr_81,