RetrogeneDB ID: retro_pvam_963

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_19359:13029..13682(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS9
• Ensembl ID: ENSPVAG00000000927
• Aliases: None
• Description: mitochondrial ribosomal protein S9 [Source:HGNC Symbol;Acc:14501]

Sequence

>retro_pvam_963
GCTCCCTGTGTGTCTTGCGGTGCCACAGTTTTCTACTATCTCATTCTTGGGGGAATGGTTAGTATGGTCCTGAGACAAGG
CCTCTGGGAATCCATAGCTGCTGAATTGCAAACAGGTTCTAGATCCCGGATACTAAGGCTAAAATATAACACAATTCTAA
CAACGAAGAAAAATGTTGCAGCCTTATGTCATGAAACTTACACAGTGGATTTTATTGAAAAGCAGATTGAAGAGTTCAAC
ATAGGAAAGAGACTTTTAGACAACATGAGGGAAAAAGATCCAGAAACTTTTACAGAGGATATTATTGATAGAGTTATTGT
TTACCTTTTTTCCTCAGTGTTTTATTTGAGCAGCAAGCCAGGAAAACACTGAAAAGATTTTTTTTTTTTTCCCCCAAAAC
AAAGAGCAAAACAGTAGGGAGAAGATAACTGTCCATTTCATCTTTTTTTTATACTAGCAAGCAATCATATTATTAATGAA
TGCATGGCACATATAGAAAACTGCTTGATGTAGAAAAATATCAAAATCAGTTGTGAGCCAAAGGCGTATTTACAGAAAAA
GCTAAAACTAAAAACATGATGGGTAATTAAGGAGGAATTAGAAGAAACATTAGTAGAAAAACTGTCAGATCAAGATCATA
CGCAGTTTATTCA

Alignment

ORF - retro_pvam_963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.94 %
• Parental protein coverage: 54.34 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ASCVSSGAAISSRLLLRGRVSLAPGQGLWKAPTADLQTGFASQILRLRHTTVVTTKKNVAALRREMYTAD
          A.CVS.GA.....L.L.G.VS....QGLW....A.LQTG..S.ILRL...T..TTKKNVAAL..E.YT.D
Retrocopy APCVSCGATVFYYLILGGMVSMVLRQGLWESIAAELQTGSRSRILRLKYNTILTTKKNVAALCHETYTVD

Parental  FIKKQIEEFNIGKRHLANMMGEDPETFTQEDIDRAIAYL-FP-SGLFEKRARPIMKHPEHIFPK-QRATQ
          FI.KQIEEFNIGKR.L.NM...DPETFT...IDR.I.YL.FP.S.LFE..AR...K......PK.QRA.Q
Retrocopy FIEKQIEEFNIGKRLLDNMREKDPETFTEDIIDRVIVYL>FP>SVLFEQQARKTLKRXXXXXPK>QRAKQ

Parental  WGEDGRPFHFLFY-TGKQSYYSLMHDTY-GLLDVEKHQ-IVRAKDLFSE--KTKDLIGSRWLIKEELEEM
          .GED..PFH.....T.KQSYY..MH.TY..LLDVEK.Q....AK..F.E..KTK...G....I.......
Retrocopy *GEDNCPFHXXXI<TSKQSYY**MHGTYRKLLDVEKYQNQL*AKGVFTEKAKTKNMMGN*GGIRRNISRK

Parental  LVEKLSDQDYA
          .V...S...Y.
Retrocopy TVRSRSYAVYS

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_963 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
Canis familiaris	ENSCAFG00000002122	1 retrocopy	retro_cfam_519,
Callithrix jacchus	ENSCJAG00000008156	1 retrocopy	retro_cjac_40,
Otolemur garnettii	ENSOGAG00000007255	1 retrocopy	retro_ogar_3314,
Pteropus vampyrus	ENSPVAG00000000927	1 retrocopy	retro_pvam_963 ,