RetrogeneDB ID: retro_pvam_587

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3905:95370..96117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN3
• Ensembl ID: ENSPVAG00000015316
• Aliases: None
• Description: ataxin 3 [Source:HGNC Symbol;Acc:7106]

Sequence

>retro_pvam_587
ATTACTAGTGAAGACTATCGCACATTTTCCAGCAGCCTTGTGGAAATATAGATGACAGTGGTTTTTTTCTCTATTCCAGT
TATAAGCAATGCCTTGAAAGTTTGGAGTGTGGAACTAATCCTGTTCAACAGTCAAGAGTATCAGAGGCTTCGGATTGATC
CCATAAATGAAAGATCATTTATATGCAATTATAAAGAACACTGATTTACAGTTAGAAAATTAGGAAAACAGTGGTTCAAC
TTGAATTCTCTCTTGATGGGTCCAGAATTAATATCGGACACATACTTTTCATTGTTCTTGGCTCACTTACAATAGGAAGG
TTATTCTGTATTTGTTCTTAAGGGTAATCTGCCAGATTGTGAAGCGGACCAACTCCTGCAGAAGCTCAGGGTCCAACAGA
TGCATCAACCAAAACGTATTGGAGTAGAATTAGCACAACAAAAAGAACAGAGAGTCCAGAAAACAGATCTGGAATGAATC
TTGGAAGCAAATGATAGGTCAGGAATGTTAGACGAAGATAAGAAGGATTTGTGTCGGGCTCTGGTATTAAGTTGCCAACA
AATTGACATGGAAGATAAAGAAGCAAATCTCTGCAGGGCTATTCAGCTCAGTATGCAAAGTAGTTCCAGAAATATATCTC
AAGATATTCCACAGACATCAGGTACACATTTTACTTAAGAAGAGCTACAGAAAAGAGAAGCCTACTTTGAAAAGCAGCAG
CAGCAGCAGGAGGATCCACCAGAACAG

Alignment

ORF - retro_pvam_587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.56 %
• Parental protein coverage: 69.25 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTSEDYRTF-LQQRSGNMDDSGFF-SIQVISNALKVWGLELILFNSPEYQRLGIDPINERSFICNYKEHW
          .TSEDYRTF..QQ..GN.DDSGFF.SI.VISNALKVW..ELILFNS.EYQRL.IDPINERSFICNYKEH.
Retrocopy ITSEDYRTF<FQQPCGNIDDSGFF>SIPVISNALKVWSVELILFNSQEYQRLRIDPINERSFICNYKEH*

Parental  FTVRKLGKQWFNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGELPDCEADQLLQMIRVQQMHRPK
          FTVRKLGKQWFNLNSLL.GPELISDTY..LFLA.LQ.EGYS.FV.KG.LPDCEADQLLQ..RVQQMH.PK
Retrocopy FTVRKLGKQWFNLNSLLMGPELISDTYFSLFLAHLQ*EGYSVFVLKGNLPDCEADQLLQKLRVQQMHQPK

Parental  LIGEELAQLKEQRVQKTDLERVLEGNDGSGMLDEDEEDLQRALALSRQQIDMEDEEADLRRAIQLSMQGS
          .IG.ELAQ.KEQRVQKTDLE..LE.ND.SGMLDED..DL.RAL.LS.QQIDMED.EA.L.RAIQLSMQ.S
Retrocopy RIGVELAQQKEQRVQKTDLE*ILEANDRSGMLDEDKKDLCRALVLSCQQIDMEDKEANLCRAIQLSMQSS

Parental  SRNISQDIPQTSGTHLTSEELRKRREAYFEKQQQQQQQQQQQ
          SRNISQDIPQTSGTH.T.EEL.K.REAYFEKQQQQQ.....Q
Retrocopy SRNISQDIPQTSGTHFT*EELQK-REAYFEKQQQQQEDPPEQ

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_587 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005786	2 retrocopies	retro_btau_1652, retro_btau_330,
Choloepus hoffmanni	ENSCHOG00000005302	1 retrocopy	retro_chof_2238,
Callithrix jacchus	ENSCJAG00000018025	2 retrocopies	retro_cjac_1724, retro_cjac_375,
Cavia porcellus	ENSCPOG00000010887	1 retrocopy	retro_cpor_1460,
Monodelphis domestica	ENSMODG00000002006	2 retrocopies	retro_mdom_1498, retro_mdom_1573,
Pteropus vampyrus	ENSPVAG00000015316	2 retrocopies	retro_pvam_1201, retro_pvam_587 ,