RetrogeneDB ID: retro_ogla_21

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 8:18984005..18985535(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA08G0175300
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA08G0175000
• Aliases: None
• Description: None

Sequence

>retro_ogla_21
ATGGAGCGCGAGGCGTGGCTGCTATGTGCAGTGCTCGCCGCGGCGACGGTCGTCTACTACCTCGCCTGCACGACGTCGCG
CCGCGCACGGCGGCGGCGTCTGCCTCCTGGCCCGACGCCGCTGCCGGTGATCGGCAACGTGCTCGGACTGCGCGGCAACA
TGCATCACGCGCTGGCGCGCCTCGCGCGCGAGCGGTACGGCCCCGTGATGACGCTGAAGCTGGGACTCGTCACCGCCGTG
GTCGTCTCGTCGCCCGGCGCGGCGAGGGAAGCGTTCACCAGGCACGACCGGCGCCTCGCGGCGCGCACGGTGCCGGACAT
CAGCCGCGCGCGCGGGCTCGCCGGCCGGTCCATGATATGGCTGCCGAGCTCCGACCCGCGCTGGAAGACGCTGCGCGGCG
TGGTGGCCGCGCACGTCTTCTCGCCACGGAGCCTCGCCGCGGCGCGCGGCGTCCGCGAGCGCAAGGTGCGCGACATCGTC
GGCTACTTCGCCGTGCACGCGGGGGAGGCGGTCGACGTCGGCGAGGCCGTGTACGGCGGCGTGATCAACCTCGTGTCGAA
CGCCTTCTTCTCCGCCGATGTGGTTGACGTCGGCAAGGAGTCAGCGCACGGGTTAAGGAAAACCGTGGAGGACATGATCT
CGGCGATCGCGAAGCCGAACGTCTCCGACCTTTTCCCCTTCCTCCGCCCTCTCGACCTGCAGGGATGGCGCCGCTGGGCG
GAGAAGCGCATCGACGAAATCTACGGCATCTTGGATGACAAAATCAACAGCCGCTTGGCCGACACCGACGCCGACGCCTC
GACGAAGAAGCACGGCGACTTCCTGGACTCCCTCCTCGAGCTCATGTCCGCCGGCAAGATTGCCCGCGACGACGTGACCA
ACATAATGTTTGAGGTCTTCGGCGCCGGGACCGACACGATCTCCATCACGGTGGAGTGGGCAATGGCGGAGCTGCTCCGC
AACCCGAGCATAATGGCGAAGGTGCGCGCGGAGATGGATGACGTCCTCGCCGGCAAGAAAACCATCGAGGAGAACGACAC
TGAAAAGCTGCCGTACCTCCGGGCCGTGATAAAGGAGGCAATGCGGCTTCACCCGGTGGCGCCGATCCTCCTACCGCACC
ATGCGGCAGAGGACGGCGTGGAGATCAGCGGCTACGCCGTGCCGAAGGGGTCGACGGTGATCTTCAACGTGTGGGCGATC
ATGCGTGACCCGATGGCGTGGGAGAGGCCGGACGAGTTCATGCCAGAGAGATTCCTGCAAAGAGCAGAGGTGGATTTCCG
AGGAAAAGACTTCGAGTTCATGCCGTTCGGGGCCGGAAGGAGGCTGTGCCCGGGGTTGCCGATGGCAGAGCGCGTCGTGC
CATTCATACTGGCGTCGCTGCTGCACGCGTTCGAGTGGAGGCTCCCCGACGGCATGTCGGCTGAGGAGTTGGATGTCAGT
GAGAAGTTCACCACAGCCAATGTTCTTACTGTCCCACTCAAGGCCGTCCCTATACTTGCCTCTAGTGCTAGTGAACTACA
AGCAAGCTAG

Alignment

ORF - retro_ogla_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.94 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEREAWLLCAALAAAMVYYYYYYHLACTTRRA--QRRLPPGPTPLPVIGNVLSLSGDMHHELARLAREQY
          MEREAWLLCA.LAAA.V.....Y.LACTT.R....RRLPPGPTPLPVIGNVL.L.G.MHH.LARLARE.Y
Retrocopy MEREAWLLCAVLAAATVV----YYLACTTSRRARRRRLPPGPTPLPVIGNVLGLRGNMHHALARLARERY

Parental  GPVMTLKLGLVTAVVVSSPDAAREAFTKHDRRLAARTVPDISRARGLTGRSMIWLPSSDPRWKTLRSAVA
          GPVMTLKLGLVTAVVVSSP.AAREAFT.HDRRLAARTVPDISRARGL.GRSMIWLPSSDPRWKTLR..VA
Retrocopy GPVMTLKLGLVTAVVVSSPGAAREAFTRHDRRLAARTVPDISRARGLAGRSMIWLPSSDPRWKTLRGVVA

Parental  THFFSPRSLTAARGVRERKVRDIVNYFAGHAAEVIDVSEAVYGGVINIVSNAFFSADVVDVGKESAHGLR
          .H.FSPRSL.AARGVRERKVRDIV.YFA.HA.E..DV.EAVYGGVIN.VSNAFFSADVVDVGKESAHGLR
Retrocopy AHVFSPRSLAAARGVRERKVRDIVGYFAVHAGEAVDVGEAVYGGVINLVSNAFFSADVVDVGKESAHGLR

Parental  ETLEDIILAIAKPNVSDLFPFLRRLDLQGWRRWAEKRYDKVFGILDDKINSRLADADADASTKKHGDFLD
          .T.ED.I.AIAKPNVSDLFPFLR.LDLQGWRRWAEKR.D...GILDDKINSRLAD.DADASTKKHGDFLD
Retrocopy KTVEDMISAIAKPNVSDLFPFLRPLDLQGWRRWAEKRIDEIYGILDDKINSRLADTDADASTKKHGDFLD

Parental  SLLELMSAGKIACDDVTTVMFDAFGARIDTISNTVVWAMAELLRNPSIMAKVRAEMEDVLAGKKTIEEND
          SLLELMSAGKIA.DDVT..MF..FGA..DTIS.TV.WAMAELLRNPSIMAKVRAEM.DVLAGKKTIEEND
Retrocopy SLLELMSAGKIARDDVTNIMFEVFGAGTDTISITVEWAMAELLRNPSIMAKVRAEMDDVLAGKKTIEEND

Parental  TEKLSYLRAVIKEAMRLHPVAPILLPHRAAEDGVEIGGYAVPKDSTVIFNVWAIMRDPTAWERPEEFMLE
          TEKL.YLRAVIKEAMRLHPVAPILLPH.AAEDGVEI.GYAVPK.STVIFNVWAIMRDP.AWERP.EFM.E
Retrocopy TEKLPYLRAVIKEAMRLHPVAPILLPHHAAEDGVEISGYAVPKGSTVIFNVWAIMRDPMAWERPDEFMPE

Parental  RFLQRAEVDFRGKDFEFIPFGAGRRLCPGLPMAERVVPFILASLLHAFEWRLPVGVAAETLDLSEKFTTV
          RFLQRAEVDFRGKDFEF.PFGAGRRLCPGLPMAERVVPFILASLLHAFEWRLP.G..AE.LD.SEKFTT.
Retrocopy RFLQRAEVDFRGKDFEFMPFGAGRRLCPGLPMAERVVPFILASLLHAFEWRLPDGMSAEELDVSEKFTTA

Parental  NALVTPLKAIPILAS
          N.L..PLKA.PILAS
Retrocopy NVLTVPLKAVPILAS

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_21 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA08G0175000	1 retrocopy	retro_ogla_21 ,