RetrogeneDB ID: retro_ogla_47

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 1:10263249..10264556(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA01G0220100
• Aliases: None
• Description: None

Sequence

>retro_ogla_47
ATTAATGTAACTTGTGAGGTACAACAATTATTAGGAAATAATCGAGTTAGAGCTGTAGCTATGAGTGCTACAGATGGGTT
GATGAGAGGAATGGAAGTGATTGACACGGGAGCTCCTCTCAGTGTTCCTGTCGGTGAAGCTACTCTTGGATGAATTTTCA
ACATTCTTGGGGAGCCTGTTGACAATTTGGGTCCTGTAGATACTAGTGCAACATTCCCTATTCATAGATCCGCGCCCGCC
TCTATCGAGTTAGATACGAAATTATCCATCTTTGAAACTGGTATTAAGGCGGTCGATCTTTTAGCTCCTTATCAGCGTGG
AGGAAAAATCGGACTATTTGGGGGAGCTGGAGTAGGTAAAACAATACTCATCATGGAATTAATCAACAATATTGCTAAAG
CTCACGGGGGCGTATCCGTATTTGGCGGAGTAGGGGAACGGACTCGTGAAGGAAATGATCTTTATATGGAAATGAAGGAA
TCTGGAGTAATTAATGAAAAAAATCTTGAGGAATCAACGGTAGCTCTAGTCTATGGCCAAATGAATGAACCGCCAGGAGC
TCGTATGAGAGTTGGTTTGACTGCCCAAACTATGGCAGAATATTTCCGAGATGTTAATAAGCAAGACGTGCTTCTATTCA
TCGATAATATCTTTCGTTTTGTTCAAGCAGGATCGGAGGTATCTGCCTTATTAAGGAGAATGCCCTCTGCAGTGGGTTAT
CAACCTACTCTTAGTACAGAAATGGGTTCTTTGCAAGAAAGAATTACTTATACTAAAAAGGATCTATAACTTCGATCCAA
GCGGTTTATGTACCTGCGGATGATTTGACCGACCCTGCTCATGCTATAACATTTGCACATTTGGATGCTACTACCGTACT
TTCCAGAGGATTAGCATCCAAAGGGATTTATCCTGCAGTAGATCCTTTAGATTCAACCTCAACTATGTTACAACCTTGGA
TCGTTGGCAACGAACATTATGAAACTGCGCAAAGAGTTAAGCAAACTTTACAACGTTACAAAGAACTTCAGGACATTATC
GCAATTCTTAGGTTGGATGAATTATCGGAGGAGGATCGTTTAACTGTAGCAAGAGCACGAAAAATTGAGCGCTTCTTATC
ACAACCGTTTTTTGTGGCAGATGTTTTTACCAGTTCTCCGGGAAAGTATGTTGGTCTTGCAGAAACTATTAGGGGATTTC
AACTAATCCTTTCCGGAGAATTAGACGTCCTACCCGAACAGGCTTTTTATTTGGTGGGTAACATCGATGAAGCTAGCACG
AAAGCTATAAACTTAGAAGAGGAGAAC

Alignment

ORF - retro_ogla_47 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.72 %
• Parental protein coverage: 78.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRLVLEVAQHLGENMVRTIAMDGTEGLVRGQRVLNTGSPITVPVGRATLGRIMNVIGEPIDEKGDITTNH
          I....EV.Q.LG.N.VR..AM..T.GL.RG..V..TG.P..VPVG.ATLG.I.N..GEP.D..G...T..
Retrocopy INVTCEVQQLLGNNRVRAVAMSATDGLMRGMEVIDTGAPLSVPVGEATLG*IFNILGEPVDNLGPVDTSA

Parental  FLPIHREAPAFVEQATEQQILVTGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELINNVAKAHGGFSV
          ..PIHR.APA..E..T...I..TGIK.VDLLAPYQRGGKIGLFGGAGVGKT.LIMELINN.AKAHGG.SV
Retrocopy TFPIHRSAPASIELDTKLSIFETGIKAVDLLAPYQRGGKIGLFGGAGVGKTILIMELINNIAKAHGGVSV

Parental  FAGVGERTREGNDLYREMIESGVIKLGDKQSESKCALVYGQMNEPPGARARVGLTGLTVAEHFRDAEGQD
          F.GVGERTREGNDLY.EM.ESGVI.......ES..ALVYGQMNEPPGAR.RVGLT..T.AE.FRD...QD
Retrocopy FGGVGERTREGNDLYMEMKESGVINXXXLE-ESTVALVYGQMNEPPGARMRVGLTAQTMAEYFRDVNKQD

Parental  VLLFIDNIFRFTQANSEVSALLGRIPSAVGYQPTLATDLGGLQERITTTKK-GSITSVQAIYVPADDLTD
          VLLFIDNIFRF.QA.SEVSALL.R.PSAVGYQPTL.T..G.LQERIT.TKK.GSITS.QA.YVPADDLTD
Retrocopy VLLFIDNIFRFVQAGSEVSALLRRMPSAVGYQPTLSTEMGSLQERITYTKK<GSITSIQAVYVPADDLTD

Parental  PAPATTFAHLDATTVLSRQISELGIYPAVDPLDSTSRMLSPHVLGEDHYNTARGVQKVLQNYKNLQDIIA
          PA.A.TFAHLDATTVLSR.....GIYPAVDPLDSTS.ML.P...G..HY.TA..V...LQ.YK.LQDIIA
Retrocopy PAHAITFAHLDATTVLSRGLASKGIYPAVDPLDSTSTMLQPWIVGNEHYETAQRVKQTLQRYKELQDIIA

Parental  ILGMDELSEDDKLTVARARKIQRFLSQPFHVAEVFTGAPGKYVELKESVQSFQGVLDGKYDDLPEQSFYM
          IL..DELSE.D.LTVARARKI.RFLSQPF.VA.VFT..PGKYV.L.E....FQ..L.G..D.LPEQ.FY.
Retrocopy ILRLDELSEEDRLTVARARKIERFLSQPFFVADVFTSSPGKYVGLAETIRGFQLILSGELDVLPEQAFYL

Parental  VGGIDEVIAKAEKIAKES
          VG.IDE...KA.....E.
Retrocopy VGNIDEASTKAINLEEEN

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_47 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00006p00059970	1 retrocopy	retro_atri_7,
Arabidopsis thaliana	AT5G08670	1 retrocopy	retro_atha_12,
Oryza sativa indica	BGIOSGA017602	2 retrocopies	retro_oind_104, retro_oind_87,
Brassica rapa	Bra006013	2 retrocopies	retro_brap_51, retro_brap_57,
Chlamydomonas reinhardtii	CHLREDRAFT_78348	1 retrocopy	retro_crei_1,
Aegilops tauschii	F775_32946	1 retrocopy	retro_atau_18,
Hordeum vulgare	MLOC_70791	1 retrocopy	retro_hvul_13,
Oryza glaberrima	ORGLA01G0220100	1 retrocopy	retro_ogla_47 ,
Triticum aestivum	TRAES3BF058700080CFD_g	2 retrocopies	retro_taes_170, retro_taes_31,