RetrogeneDB ID: retro_pvam_1201

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_4099:95140..95925(+)
• 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_1201
ATGGAAGCCATCTTCCACAAGAGACAAGAAGGCTCACTTTGTGCTCAACATTGCTTGAATAATCTGTTGGCAAGGAGACT
ATTTCATCCCTGTAGAACTATTGCACATTGACTAGATAAAGAAGAGAGGATGAGAATGGCAGAAGGAGGAATTACTCATG
AGGACTATTACACATTTTTATAGCAGCCTTCTGGAAATATGGATGACAGTGTTTTTTTCTCTATTCGAGTTATAAATAAT
GCCTTGAAAATTTGGGGCATAGAACTAATCCTATTCAACAGTCCAGAGTATCAGAGGTTTGGTATTGATTCCATAAATGA
AAAATCATTTATATCAATTATAAAGAACCCTAGTTTACAGTTAGAAAATTCAGAAAACAGTGGTGTAACTTCAAGTCTCT
CTTGACAGGTCCAGAATTAATAACAAACACATACCTTGCAGCTTTCTTGAATCAATTATAACAGGAAGTTGTTCTATATT
TGTTGTTAAGGGTGATCTGCCAGATTGTGAAGCTGACCAACTCCTGCAGATGGTCAGGGGTCCAACAGATGCATCTACCA
AAACTTATTGGAGAAGAATTAGCACAACTAAAAGAACAGAGAGTCCAGAAAACATATCTGGAATGAGTCTTAGAAGAAAA
TGATGGGTCAGGAATATTAGACAAAGATGAAGAGGATTTGCAGCAGGCTATAGCACTAAATCACCAACAAATTGACATAA
AAGATGAAGAAGAAGATCTCCATAGGGCTATTCAGCTCAGTATACAAGGTAGTTGCAGAAATATA

Alignment

ORF - retro_pvam_1201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.03 %
• Parental protein coverage: 73.13 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQRSGNMD
          ME.IFH..QEGSLCAQHCLNNLL....F.P.....IAH.LD.EERMRMAEGG.T.EDY.TFL.Q.SGNMD
Retrocopy MEAIFHKRQEGSLCAQHCLNNLLARRLFHPCR--TIAH*LDKEERMRMAEGGITHEDYYTFL*QPSGNMD

Parental  DSGFFSIQVISNALKVWGLELILFNSPEYQRLGIDPINERSFI-CNYKEHWFTVRKLGKQWFNLNSLLTG
          DS.FFSI.VI.NALK.WG.ELILFNSPEYQR.GID.INE.SFI..NYKE..FTVRK..KQW.N..SLLTG
Retrocopy DSVFFSIRVINNALKIWGIELILFNSPEYQRFGIDSINEKSFI<INYKEP*FTVRKFRKQWCNFKSLLTG

Parental  PELISDTYLALFLAQLQQE-GYSIFVVKGELPDCEADQLLQMIR-VQQMHRPKLIGEELAQLKEQRVQKT
          PELI..TYLA.FL.QL.QE...SIFVVKG.LPDCEADQLLQM.R.VQQMH.PKLIGEELAQLKEQRVQKT
Retrocopy PELITNTYLAAFLNQL*QE<SCSIFVVKGDLPDCEADQLLQMVR>VQQMHLPKLIGEELAQLKEQRVQKT

Parental  DLERVLEGNDGSGMLDEDEEDLQRALALSRQQIDMEDEEADLRRAIQLSMQGSSRNI
          .LE.VLE.NDGSG.LD.DEEDLQ.A.AL..QQID..DEE.DL.RAIQLS.QGS.RNI
Retrocopy YLE*VLEENDGSGILDKDEEDLQQAIALNHQQIDIKDEEEDLHRAIQLSIQGSCRNI

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_1201 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,