RetrogeneDB ID: retro_pvam_426

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_307:43795..44167(-)
• Located in intron of: ENSPVAG00000004606

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS25
• Ensembl ID: ENSPVAG00000012492
• Aliases: None
• Description: ribosomal protein S25 [Source:HGNC Symbol;Acc:10413]

Sequence

>retro_pvam_426
ATGTCGCTTGAGGATGACGAGAAGATAAAAGATGCCGAAAGTCAGCCAAGAAAGACAAAGATCCAGTGAACAAATCCCGG
GTCAAGGCCAAAATGAAGTGGTCCAAAGGCAATGTCCAGGACAAGCTCAAAACCTAGTCTTGTTTGACAAAGCGACATAT
GACAAACTCTGGAAAGAAATTCCCAACTCTAAGCTTATGACCCCAGCCGTCTGTCATCTCTGAGAGCCTGAAGATCTGGG
GACCATCGGTGGAACAGCCCTTCAGGAGCTCCTTCGTAAAGGGCGTGTAGAACTAGTTCAAAGCACAGAGTTCCAGTAAT
TTCCACCAGAAACACCGAGGGAGGGGGGACCCCAGCCGCGGGTGAGGATGCA

Alignment

ORF - retro_pvam_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.89 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MPPKDDKKKKDAG-KSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLN-NLVLFDKATYDKLC-KEVPNYKL
          M...DD.K.KDA..KSAKKDKDPVNKS..KAK.K.WSKG.V.DKL..NLVLFDKATYDKL..K..P...L
Retrocopy MSLEDDEKIKDAE<KSAKKDKDPVNKSRVKAKMK-WSKGNVQDKLK<NLVLFDKATYDKLW>KKFPTLSL

Parental  -ITPAVVSERLKI-RGSLARAALQELLSKGLIKLV-SKHRAQVIYTRNTKGGDAPAAGEDA
          ...P.V.SE.LKI..G.....ALQELL.KG...LV.SKHR..VI.TRNT.GG..PAAGEDA
Retrocopy *PQPSVISESLKI<LGTIGGTALQELLRKGRVELV<SKHRVPVISTRNTEGGGTPAAGEDA

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_426 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 6 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027772	2 retrocopies	retro_btau_203, retro_btau_9,
Callithrix jacchus	ENSCJAG00000013691	1 retrocopy	retro_cjac_208,
Dasypus novemcinctus	ENSDNOG00000007880	7 retrocopies	retro_dnov_1092, retro_dnov_1566, retro_dnov_2219, retro_dnov_2593, retro_dnov_346, retro_dnov_877, retro_dnov_973,
Mus musculus	ENSMUSG00000009927	15 retrocopies	retro_mmus_128, retro_mmus_1368, retro_mmus_1455, retro_mmus_1760, retro_mmus_1769, retro_mmus_1788, retro_mmus_2375, retro_mmus_2393, retro_mmus_2641, retro_mmus_2700, retro_mmus_2797, retro_mmus_3218, retro_mmus_336, retro_mmus_3523, retro_mmus_880,
Otolemur garnettii	ENSOGAG00000007265	3 retrocopies	retro_ogar_220, retro_ogar_257, retro_ogar_32,
Pteropus vampyrus	ENSPVAG00000012492	12 retrocopies	retro_pvam_1066, retro_pvam_1176, retro_pvam_1202, retro_pvam_1287, retro_pvam_130, retro_pvam_1418, retro_pvam_1448, retro_pvam_247, retro_pvam_277, retro_pvam_426 , retro_pvam_653, retro_pvam_668,