RetrogeneDB ID: retro_ogar_125

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873685.1:840849..841809(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000029165
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SOX3
• Ensembl ID: ENSOGAG00000025781
• Aliases: None
• Description: SRY (sex determining region Y)-box 3 [Source:HGNC Symbol;Acc:11199]

Sequence

>retro_ogar_125
ATGTACAACATGATGGAGACGGAGCTGAAGCCGCCGGGCCCGCAGCAAACTTCGGGGGGCGGCGGCGGCGGCGGCAACTC
CACCGCGGCGGCGGCGGGCGGCAACCAGAAGAACAGCCCGGACCGCGTCAAGCGGCCCATGAATGCCTTCATGGTGTGGT
CCCGCGGGCAGCGGCGCAAGATGGCCCAGGAAAACCCCAAGATGCATAACTCGGAGATCAGCAAGCGCCTGGGCGCCGAG
TGGAAACTTTTGTCGGAGACGGAGAAACGGCCTTTCATCGACGAGGCCAAGCGGCTGCGAGCCCTGCACATGAAGGAGCA
CCCGGATTATAAATACCGGCCCCGGCGGAAAACCAAGACGCTCATGAAGAAGGATAAGTACACGCTGCCCGGCGGGCTGC
TGGCCCCCGGCGGCAACAGCATGGCGAGCGGGGTCGGGGTGGGCGCCGGCCTGGGCGCGGGCGTGAATCAGCGCATGGAC
AGTTACGCGCACATGAACGGCTGGAGCAATGGCAGCTACAGCATGATGCAGGACCAGCTGGGCTACCCGCAGCACCCGGG
CCTCAATGCTCACGGCGCCGCGCAGATGCAGCCCATGCACCGCTACGACGTGAGCGCCCTGCAGTACAACTCCATGACCA
GCTCGCAGACCTACATGAACGGCTCGCCCACCTACAGCATGTCCTACTCACAGCAGGGCACCCCTGGCATGGCTCTGGGC
TCCATGGGTTCGGTGGTCAAGTCCGAGGCCAGCTCCAGCCCCCCTGTGGTTACCTCTTCCTCCCACTCCAGGGCGCCCTG
CCAGGCCGGGGACCTCCGGGACATGATCAGCATGTACCTCCCCGGCGCCGAGGTGCCGGAACCCGCCGCCCCCAGCAGAC
TTCACATGTCTCAGCACTACCAGAGCGGCCCGGTGCCCGGCACGGCCATTAACGGCACACTGCCCCTCTCGCACATGTGA

Alignment

ORF - retro_ogar_125 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYSLLETELKNPVGTPTPAAATGGPSAPGGAGSSGSASGGGGGSDQDRVKRPMNAFMVWSRGQRRKMALE
          MY...ETELK.....P.P....GG....GG..S...A.GG......DRVKRPMNAFMVWSRGQRRKMA.E
Retrocopy MYNMMETELK----PPGPQQTSGGGG--GGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMAQE

Parental  NPKMHNSEISKRLGADWKLLTDAEKRPFIDEAKRLRAVHMKEYPDYKYRPRRKTKTLLKKDKYSLPGGLL
          NPKMHNSEISKRLGA.WKLL...EKRPFIDEAKRLRA.HMKE.PDYKYRPRRKTKTL.KKDKY.LPGGLL
Retrocopy NPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLMKKDKYTLPGGLL

Parental  PPGAAAAAAAAAAAAAASSPVGVGQRLDTYTHVNGWANGAYSLVQEQLGYAQPPSMSSPPPPPALPQMHR
          .PG....A......A......GV.QR.D.Y.H.NGW.NG.YS..Q.QLGY.Q.P...........P.MHR
Retrocopy APGGNSMASGVGVGAGLGA--GVNQRMDSYAHMNGWSNGSYSMMQDQLGYPQHPGLNAHGAAQMQP-MHR

Parental  YDMAGLQYSPMMPPGAQSYMNAAAAAAAASGYGGMAPSAAMSLGPMGSVVKSEPSSPPPAI--ASHSQRA
          YD...LQY..M.....Q.YMN............G......M.LG.MGSVVKSE.SS.PP.....SHS...
Retrocopy YDVSALQYNSM--TSSQTYMNGSPTYSMSYSQQG---TPGMALGSMGSVVKSEASSSPPVVTSSSHSRAP

Parental  C-LGDLRDMISMYLPPGGDAADAASPLPGGRLHGVHQHYQGA---GTAVNGTVPLTHI
          C..GDLRDMISMYL.PG......A.P....RLH...QHYQ.....GTA.NGT.PL.H.
Retrocopy CQAGDLRDMISMYL-PGAEVPEPAAP---SRLH-MSQHYQSGPVPGTAINGTLPLSHM

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_125 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	ENSOGAG00000025781	1 retrocopy	retro_ogar_125 ,