RetrogeneDB ID: retro_ogla_40

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 4:13588222..13589260(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA04G0096300
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA01G0092400
• Aliases: None
• Description: None

Sequence

>retro_ogla_40
ATGGCGGCGACATTGCGTTGGGGCGGCGGCGGGCTCGCGGTGGCGGCGTTTGCGGCGGTGGTCGCGTTGTCCGGCCTCCT
CGGCGTCGCGGCGAACTACGGCGGCGGCGGCGGGTTCTTGTTCCCGCAGTTCTATCAGCACACGTGCCCGCAGATGGAGG
CGGTGGTGGGCGGCATCGTGGCGAGGGCGCACGCAGAGGACCCGCGCATGGCGGCGTCGCTGCTGCGGATGCACTTCCAC
GACTGCTTCGTGCAGGGGTGCGACGCGTCGGTGCTGCTCGACGCCGACGGCAGCGGGCGGTTCGCCACGGAGAAGCGGTC
CAACCCCAACCGCGACTCGCTGCGCGGGTACGAGGTGATCGACGAGATCAAGGCCGCCCTGGAGCACGCGTGCCCGCGCA
CCGTCTCCTGCGCCGACATCGTCGCCGTCGCCGCCAGGGACTCCACCGCGCTCACCGGCGGGCCGTGGTGGGAGGTGCCC
CTCGGCAGGCGGGACTCGCTGACGGCCAGCCTGAGCGGCTCCAACAACCTCATCCCGGCGCCCAACGACACGCTCCCCAC
CATCGTCGGCAAGTTCCGCAACCAGGGCCTCGACGTCGTCGACCTCGTCGCGCTCTCCGGCGGCCACACCATCGGCAACT
CCCGGTGCGTCAGCTTCCGCCAGAGGCTGTACGGCCAGCTGAACAGCGACGGGAAGCCGGACTTCACCCTGAACCCGGCG
TACGCGGCGGAGCTCCGGGAGCGGTGCCCGAGCTCCGGCGGCGACCAGAACCTGTTCGCGCTGGACCCGGCCAGCCAGTT
CCGGTTCGACAACCAGTACTACCGCAACATCCTCGCCATGAACGGCCTCCTCAGCTCCGACGAGGTGCTCCTCACCAAGA
GCCGGGAGACGATGGAGCTCGTCCACCGCTACGCCGCCAGCAACGAGCTCTTCTTCGCGCAGTTCGCCAAGTCCATGGTC
AAGATGGGCAGCATCTCCCCGCTCACCGGCCACAACGGCGAGATCAGGATGAACTGCAGGAGGGTCAACCACTTCTAG

Alignment

ORF - retro_ogla_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.77 %
• Parental protein coverage: 91.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YGYGYG-LFPQFYDHSCPKAKEIVQSIVAQAVARETRMAASLVRLHFHDCFVKGCDASVLLD--NSTTII
          YG.G.G.LFPQFY.H.CP.....V..IVA.A.A...RMAASL.R.HFHDCFV.GCDASVLLD...S....
Retrocopy YGGGGGFLFPQFYQHTCPQMEAVVGGIVARAHAEDPRMAASLLRMHFHDCFVQGCDASVLLDADGSGRFA

Parental  SEKGSNPNMNSLRGFEVVDEIKAALEAACPGTVSCADILALAARDSTVLVGGPYWDVPLGRRDSLGASIQ
          .EK.SNPN..SLRG.EV.DEIKAALE.ACP.TVSCADI.A.AARDST.L.GGP.W.VPLGRRDSL.AS..
Retrocopy TEKRSNPNRDSLRGYEVIDEIKAALEHACPRTVSCADIVAVAARDSTALTGGPWWEVPLGRRDSLTASLS

Parental  GSNNDIPAPNNTLPTIITKFKRQGLNIVDVVALSGGHTIGMSRCTSFRQRLYNQ-SGNGMADYTLDVSYA
          GSNN.IPAPN.TLPTI..KF..QGL..VD.VALSGGHTIG.SRC.SFRQRLY.Q....G..D.TL...YA
Retrocopy GSNNLIPAPNDTLPTIVGKFRNQGLDVVDLVALSGGHTIGNSRCVSFRQRLYGQLNSDGKPDFTLNPAYA

Parental  AQLRQGCPRSGGDNNLFPLDFVSPAKFDNFYFKNILSGKGLLSSDQVLLTKSAETAALVKAYADDVNLFF
          A.LR..CP.SGGD.NLF.LD..S...FDN.Y..NIL...GLLSSD.VLLTKS.ET..LV..YA....LFF
Retrocopy AELRERCPSSGGDQNLFALDPASQFRFDNQYYRNILAMNGLLSSDEVLLTKSRETMELVHRYAASNELFF

Parental  KHFAQSMVNMGNISPLTGSQGEIRKNCRRLNNY
          ..FA.SMV.MG.ISPLTG..GEIR.NCRR.N..
Retrocopy AQFAKSMVKMGSISPLTGHNGEIRMNCRRVNHF

Legend:

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

Expression

RNA-Seq

Oryza glaberrima was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza glaberrima was not studied using ChIP-Seq data.

EST

Oryza glaberrima was not studied using EST data.

TSS

Oryza glaberrima was not studied using FANTOM5 data.

Lab

retro_ogla_40 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glaberrima 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA01G0092400	1 retrocopy	retro_ogla_40 ,
Oryza glaberrima	ORGLA03G0092500	1 retrocopy	retro_ogla_52,
Oryza glaberrima	ORGLA03G0209400	1 retrocopy	retro_ogla_23,