RetrogeneDB ID: retro_ogar_1009

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873533.1:4489166..4489931(-)
• Located in intron of: ENSOGAG00000013396

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACMSD
• Ensembl ID: ENSOGAG00000001854
• Aliases: None
• Description: aminocarboxymuconate semialdehyde decarboxylase [Source:HGNC Symbol;Acc:19288]

Sequence

>retro_ogar_1009
AAACCTCAGGACACTTTAAACTGGTGCCAGCTTTTAAACAATGACCTAGGTGCCATCACTGCAACCACCCAGGAAGTTTG
TAGGCCTGGGAATGCTGCCCATGCAGGGCCCCAGTTGGTCACTGAGGAGATGGAGTGCTATCTGAAGGAGCTGGGCTTTC
CTGGGATCCAGATCGGCTCTCACATCAACCAGTGGGATCTGAACTCACAGGAACACTTCCCTGTCTACCAGGCGGCTGAA
TGGCTGAACTGTTCCCTATTTGTGCATCCCTAGGATATGTGGTTGGACGGCTCATGGCCAAATACTGGCTTCCTTGGCTC
ATAGAAATGCCAACAGAGAACACCATAGCCATTTGCTCCACAATCACAGGTTGAGTGTTTGAGAAATTTCCTGAACTATT
AAGTGTGTTTTGCATAGGGAGGTGGTGCCTTCGCCTTCACACTGGGAAGAATCTCTCATGGATTTAGCATGAGGCCAGAT
CTGTGTGCCCAGGACAATCCAGTTAACCCAAAGAAATATCTTGGTTCCTTTTAAATGGACCTCTTGGTTCATAATCCTCT
GTCCCTCAAGCTAGAGGACAGAGCATTAACGAATGTCACAGGAAAAGATAAAGTCATTTTGGGAACTGACTACCCCTTCC
CCCTAGGTGAGCTGGAACCCAGGTAACTGAGAGAATTCATGGAAGAATTTGATGAAGAAACAAAGGATAAATTTAAAGCT
AGCAATGCCCTGGAATTTTGGGGTCTTGAGAGAAAAAACATTGAA

Alignment

ORF - retro_ogar_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.48 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KPQDTLSLCQLLNNDLAATVA-SHP-RRFVGLGTLPMQ-APELAIEEMERCVKELGFPGVQIGSHINEWD
          KPQDTL..CQLLNNDL.A..A..HP.R.FVGLG.LPMQ..P.L..EEME...KELGFPG.QIGSHIN.WD
Retrocopy KPQDTLNWCQLLNNDLGAITA<NHP<RKFVGLGMLPMQ<GPQLVTEEMECYLKELGFPGIQIGSHINQWD

Parental  LNARELFPVYAAAERLNCSLFVHPWDMQMDGR-MAKYWFPWLVGMPTETTIAVGSMIMGGVFEKFPKLK-
          LN..E.FPVY.AAE.LNCSLFVHP.DM..DG..MAKYW.PWL..MPTE.TIA..S.I.G.VFEKFP.L..
Retrocopy LNSQEHFPVYQAAEWLNCSLFVHP*DMWLDGS<MAKYWLPWLIEMPTENTIAICSTITG*VFEKFPELL>

Parental  VCFAHGGGAFAFTVGRISHGFSMRPDLCAQDNPINPKKYLGSFYTDSLVHDPLSLKL----LTDVIGKDK
          VCFA.GGGAFAFT.GRISHGFSMRPDLCAQDNP.NPKKYLGSF..D.LVH.PLSLKL....LT.V.GKDK
Retrocopy VCFA*GGGAFAFTLGRISHGFSMRPDLCAQDNPVNPKKYLGSF*MDLLVHNPLSLKLEDRALTNVTGKDK

Parental  VILGTDYPFPLGELEPGKLIESMEEFDEETKDKLKAGNALEFLGLERKQFE
          VILGTDYPFPLGELEP..L.E.MEEFDEETKDK.KA.NALEF.GLERK..E
Retrocopy VILGTDYPFPLGELEPR*LREFMEEFDEETKDKFKASNALEFWGLERKNIE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1009 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000001854	1 retrocopy	retro_ogar_1009 ,