RetrogeneDB ID: retro_pvam_308

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2460:23246..23969(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL7
• Ensembl ID: ENSPVAG00000009292
• Aliases: None
• Description: ribosomal protein L7 [Source:HGNC Symbol;Acc:10363]

Sequence

>retro_pvam_308
GAAGAGAAGAAGTTTCCTTCTGTGCCAGAAACCCCTAAGAAAAAGTGAAAGAATTTTGCAGAGCTGAAGATCAAGCTCCT
GAGAAAGAAGTTCTGCCCAAAAGATGCTTCAAAAGACAAGGAGGAAGCTTATCTATGAAAAAGCTAAGCACTATCACAAA
GAATATAGGCAGATGTACAGAACTGAGATTTGGATGGCTAGGATGGCAAGAAAAGCTGGCAACTTCTATGTACCTGCAGA
ACCCAAACTGGCATTTGCCATCAGGATCAGAGGCATCAACAGTGTGAGCCCCAAGGTCCAAAAGGTGCTGTGGCTTCTTC
TCCTTTACCAGATCTTTAATGGCACCTTTGTTAAGCTCAACAAAGCTTTGATTAACATGATGAGGACTATGGAGCCATAC
ATTGCATGGGGGTACCCAAACCTGAAGTCGGTCAATGAATTCATCTACAAGCATGGTTATGGCAAAATCAATAAAAAGCG
AATTGCCCTGACAGGAAACACATTGATTCCTCATTCTCTTGGTAAATATGGCATCATTTGCATGGAGGATCTGATTCGCG
AGATCTATACTGTTGGAAGACGCTTCAAAGAAGAAAGCTACTTCTAGAGCCCTTCGAGTTGTCTTCTCCATGAGGTGGAA
TGAAGAAAAAGACCATCCATTTTGTAGAAGATGGAAACACTGGCAATGGGGACCAGATCAACAGGCTTATTAGAAGGATG
AAC

Alignment

ORF - retro_pvam_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.79 %
• Parental protein coverage: 93.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKKKVPAVPETLKKKRRNFAELKIKRLRKKF-AQKMLRKARR-LIYEKAKHYHKEYRQMYRTEIRMARMA
          E.KK.P.VPET.KKK..NFAELKIK.LRKKF.AQKML.K.RR.LIYEKAKHYHKEYRQMYRTEI.MARMA
Retrocopy EEKKFPSVPETPKKK*KNFAELKIKLLRKKF>AQKMLQKTRRKLIYEKAKHYHKEYRQMYRTEIWMARMA

Parental  RKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGYP
          RKAGNFYVPAEPKLAF.IRIRGIN.VSPKV.KVL.LL.L.QIFNGTFVKLNKA.INM.R..EPYIAWGYP
Retrocopy RKAGNFYVPAEPKLAFAIRIRGINSVSPKVQKVLWLLLLYQIFNGTFVKLNKALINMMRTMEPYIAWGYP

Parental  NLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGKYGIICMEDLIHEIYTVGKRFKEANNF-LWPFKLS
          NLKSVNE.IYK.GYGKINKKRIALT.NTLI..SLGKYGIICMEDLI.EIYTVG.RFKE...F.L.PF.LS
Retrocopy NLKSVNEFIYKHGYGKINKKRIALTGNTLIPHSLGKYGIICMEDLIREIYTVGRRFKEESYF<LEPFELS

Parental  SPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN
          SP.GGMKKKT.HFVE.G..GN..DQINRLIRRMN
Retrocopy SP*GGMKKKTIHFVEDGNTGN-GDQINRLIRRMN

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_308 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 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Loxodonta africana	ENSLAFG00000017110	10 retrocopies	retro_lafr_140, retro_lafr_169, retro_lafr_334, retro_lafr_462, retro_lafr_47, retro_lafr_524, retro_lafr_694, retro_lafr_707, retro_lafr_816, retro_lafr_909,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Oryctolagus cuniculus	ENSOCUG00000008407	12 retrocopies	retro_ocun_109, retro_ocun_1164, retro_ocun_1282, retro_ocun_1342, retro_ocun_1494, retro_ocun_1646, retro_ocun_1879, retro_ocun_456, retro_ocun_501, retro_ocun_718, retro_ocun_727, retro_ocun_785,
Pteropus vampyrus	ENSPVAG00000008696	3 retrocopies	retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Pteropus vampyrus	ENSPVAG00000009292	10 retrocopies	retro_pvam_105, retro_pvam_109, retro_pvam_1192, retro_pvam_1221, retro_pvam_151, retro_pvam_287, retro_pvam_308 , retro_pvam_68, retro_pvam_69, retro_pvam_995,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209, retro_sscr_796,