RetrogeneDB ID: retro_ogla_76

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: ADWL01015117.1:356..872(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA01G0055400
• Aliases: None
• Description: None

Sequence

>retro_ogla_76
CTCGGCATGTTTGAAATTGGGCGACCAATGGGTAAAGGCAAATTCGGTCGCGTCTATCTCGCACGGGAGCGCAGTTCAGG
CTTCATCTGCGCCCTGAAAGTTCTCTACAAGGCTGAGTTACGACAATGCCGAATGGAAAGTCAAGTACGCCGAGAAATCG
AGATCCAGACAAATTTGCGTCACCCCAATATCGTGCAATTATACAGCTATTTCCATGATACCAAGCGCATCTTTCTCGTC
CTCGAGTTCGCGGCCAAAGGCGAGCTTTATAAGCATCTGCAAAAGGAAACTCGATTTACAGAGAAAAAAGCGGCCCGATT
TACCGCTCAAGTCGTATCAGCGCTGCAGTATCTGCACCGAAAGAACATCATCCATCGAGATATCAAGCCTGAAAATATTT
TAGTTGGTATGTATGATGAACTGAAAATCAGCGACTTTGGGTGGAGTGTCCATTCACCTTCCAGAAGGCGAGAAACGATG
TGCGGCACGCTGGACTACCTGCCTCCTGAGATGATA

Alignment

ORF - retro_ogla_76 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.63 %
• Parental protein coverage: 57.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSDFDIGKPLGRGKFGHVYLAREKRSNHIVALKVLFKSQLKQSQVEHQLRREVEIQSHLRHPNILRLYGY
          L..F.IG.P.G.GKFG.VYLARE..S..I.ALKVL.K..L.Q...E.Q.RRE.EIQ..LRHPNI..LY.Y
Retrocopy LGMFEIGRPMGKGKFGRVYLARERSSGFICALKVLYKAELRQCRMESQVRREIEIQTNLRHPNIVQLYSY

Parental  FYDQTRVYLILEYALKGELYKELQRCKHFSERRSATYIASLARALIYLHGKHVIHRDIKPENLLIGSQGE
          F.D..R..L.LE.A.KGELYK.LQ....F.E...A...A....AL.YLH.K..IHRDIKPEN.L.G...E
Retrocopy FHDTKRIFLVLEFAAKGELYKHLQKETRFTEKKAARFTAQVVSALQYLHRKNIIHRDIKPENILVGMYDE

Parental  LKIADFGWSVHTFNRRR-TMCGTLDYLPPEMV
          LKI.DFGWSVH...RRR.TMCGTLDYLPPEM.
Retrocopy LKISDFGWSVHSPSRRRETMCGTLDYLPPEMI

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_76 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA01G0055400	1 retrocopy	retro_ogla_76 ,