RetrogeneDB ID: retro_ogla_23

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 2:7178245..7179262(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA02G0090700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA03G0209400
• Aliases: None
• Description: None

Sequence

>retro_ogla_23
ATGGCGGCAATGTCTGCTTCGGGCCGGAGGGTCTTCTTGCTCGGTGCCCTTCTGCTCGTCGCCGTCTCTTGCCATGGCGG
CTTTGGCGGCGTCGGCGTGGCGGAGGGTTTGTCGACGAGGTACTATGCTAAGACGTGCCCCGCCGTGGAGTCCGTCGTTC
GGTCGGTGATGGCGCGGGCGGTGGCGGCGGACCGGCGCATGGGCGCGTCCGTGCTCAGGCTCTTCTTCCACGACTGCTTC
GTGAACGGCTGCGACGGGTCCGTCCTGCTCGACGACGCGCCGCCGGGGTTCACCGGGGAGAAGGGCGCCGGCGCGAACGC
CGGCTCCGCGCGCGGGTTCGAGGTGGTGGACGCGGCGAAGGCGCGGGTGGAGGCGGCGTGCCGCGCCACCGTGTCGTGCG
CCGACGTGCTCGCGCTCGCCGCGCGCGACGCCGTGGCGCTCCTCGGCGGGCCGACGTGGCCCGTGAGGCTGGGACGGAAG
GACGCCCGCACGGCGAGCCAGGCCGCGGCGAACGGCAACCTCCCCGGTCCGGTGTCAAGCCTCACCTCGCTGCTCGCCAC
GTTCGCCGCCAAGGGCCTTTCGGCGCGCGACATGACGGCGCTGTCGGGTGCGCACACGGTGGGGCGCGCCCGGTGCGCCA
CGTTCCGCGGCCGCGTCAACGGCGGCGACGCCAACGTGAACGCCACCTTCGCCGCCCAGCTCCGGCGCCTGTGCCCCGCG
GGCACCGGCGGCGACGGCAACCTCGCGCCGCTGGACGCCGAGACGCCCAACGTGTTCGACAACGGCTACTTCCGCGAGCT
GACGAAGCAGCGCGGGCTGCTGCACTCGGACCAGGAGCTGTTCGCCGCCGGCGGCGGCGGCAGGTCGTCGTCGCAGGACG
CGCTGGTGCGGAAGTACGCCGGCAACGGGGCGGAGTTCGCGAGGGACTTCGCCAAGGCGATGGTTAAGATGGGGAACCTC
GCGCCGGCCGCCGGGACGCCGGTGGAGGTCAGGCTCAACTGCCGGAAGCCCAACTAG

Alignment

ORF - retro_ogla_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.6 %
• Parental protein coverage: 88.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSDSYYDASCPAALLTIRTVVSAAVLLDPRMGASLLRLHFHDCFVQGCDASVLLDDTG-SFTGEKGAGPN
          LS..YY...CPA.....R.V...AV..D.RMGAS.LRL.FHDCFV.GCD.SVLLDD....FTGEKGAG.N
Retrocopy LSTRYYAKTCPAVESVVRSVMARAVAADRRMGASVLRLFFHDCFVNGCDGSVLLDDAPPGFTGEKGAGAN

Parental  AGSLRGFEVVDNAKTLLETVCPQTVSCADILAVAARDAVVQLGGPSWTVLLGRRDSTTASASLANSDLPA
          AGS.RGFEVVD.AK...E..C..TVSCAD.LA.AARDAV..LGGP.W.V.LGR.D..TAS...AN..LP.
Retrocopy AGSARGFEVVDAAKARVEAACRATVSCADVLALAARDAVALLGGPTWPVRLGRKDARTASQAAANGNLPG

Parental  PSSTLATLLAAFSNKGLTTTDMVALSGAHTIGRAQCANFRDRIY-NDTDIDASFAASLRAGCPQSGDGSG
          P.S.L..LLA.F..KGL...DM.ALSGAHT.GRA.CA.FR.R....D....A.FAA.LR..CP....G.G
Retrocopy PVSSLTSLLATFAAKGLSARDMTALSGAHTVGRARCATFRGRVNGGDANVNATFAAQLRRLCPAGTGGDG

Parental  -LAPLDESSPDAFDNGYFGGLLSQRGLLHSDQALFAGGGG----STDGQVRSYASSNDQFASDFSTAMVK
          .LAPLD...P..FDNGYF..L..QRGLLHSDQ.LFA.GGG....S.D..VR.YA.....FA.DF..AMVK
Retrocopy NLAPLDAETPNVFDNGYFRELTKQRGLLHSDQELFAAGGGGRSSSQDALVRKYAGNGAEFARDFAKAMVK

Parental  MGNISPLTGSAGEIRVNCRAVN
          MGN..P..G...E.R.NCR..N
Retrocopy MGNLAPAAGTPVEVRLNCRKPN

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_23 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 ,