RetrogeneDB ID: retro_pvam_105

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1382:365523..366151(-)
• 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_105
AAGAAGATGCTTAGAAAAGTAAGGAGGAAGCTTGTCTATGAAAAAACTAGGCAGCAGCACACAGCATGTAGGTAGATGGA
CAGGCTGAGGTGCGAATGGCTAGGATGGCATGAAAAGCTGGCTACTTCTGTGTACCCATGGAACTCAAATTGGCATTCAT
CATCGAGATCAGAGACATCGACAGTGTGAGCACAAAGGTCCAAAGCATGCTGCTGCTTCTCGCCTTCTCCAGATCTTTAA
TGGCATCTTTGTTAAGCTCGGCCAGGCTTCGATTAACATGCTGAGGCTGGTGGACCCATGGATTGCATGGGGTGCCCAAA
CCTGAAGTCAGTAAATGAATTGATCTATGAGTGTGGTTATGGCAGCAAAATCAACAAAAGCCAGGTGGCCTGAGAGAGAG
CACACTGACGGCTTCATCTCTTGGTATACATGGCATCATCTGCATGGAGGATCTGATTCACGAGATCTATACTGTTGGAA
AATGCTTCAGAGAAGCAAACGACTTCCTGTGGCCCTTCAGGTTATCTTCTCCATGAGGTGGAATGAAGAAAAAGACCACC
CGTTTGTAGAAGGTGGAGATGCTGGCAGCAGGGAAGACCAGATCAACAAGCTTATTAGAAGGATGAGC

Alignment

ORF - retro_pvam_105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.91 %
• Parental protein coverage: 81.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QKMLRKARR-LIYEKAKHYHKEYRQMYR-TEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRK
          .KMLRK.RR.L.YEK....H...R.M.R..E.RMARMA.KAG.F.VP.E.KLAF.I.IR.I..VS.KV..
Retrocopy KKMLRKVRRKLVYEKTRQQHTACR*MDR<AEVRMARMA*KAGYFCVPMELKLAFIIEIRDIDSVSTKVQS

Parental  VLQLL-RLRQIFNGTFVKLNKASINMLRIVEPYIAWGY-PNLKSVNELIYKRGYG-KINKKRIA-LTDNT
          .L.LL.RL.QIFNG.FVKL..ASINMLR.V.P.IAWG..PNLKSVNELIY..GYG.KINK...A.L...T
Retrocopy MLLLL<RLLQIFNGIFVKLGQASINMLRLVDPWIAWGA<PNLKSVNELIYECGYGSKINKSQVA<LREST

Parental  LIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTH-FVEGGDAGNREDQINR
          L.A.SLG..GIICMEDLIHEIYTVGK.F.EAN.FLWPF.LSSP.GGMKKKTT..FVEGGDAG.REDQIN.
Retrocopy LTASSLGIHGIICMEDLIHEIYTVGKCFREANDFLWPFRLSSP*GGMKKKTTR<FVEGGDAGSREDQINK

Parental  LIRRMN
          LIRRM.
Retrocopy LIRRMS

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_105 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,