RetrogeneDB ID: retro_ogla_15

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 9:17272645..17273866(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA09G0166100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA08G0054200
• Aliases: None
• Description: None

Sequence

>retro_ogla_15
ATGAACAAGTGCAGGTCTAGCAGTAGCAGTAGCAGGGCCTTGTATGCTCTCCTCCTCACTTCTCTTATACTAACAGTAAT
AGTATTGTACCTCCCGCCTCCACCTGATCCTCTTTCCCAATCCCAATTCGAATTCGACCAACTAAAGCTTGACGATCATC
CGCCGCCACCGCAGCTGCACCGCCGCAGGACGAAGCGGTGCGCCGAGCACCTCAGGTGGGCGGCCTCCCTCGCCTCTCAA
CACAATGCCACCCTCCTGCTCACCGTCGATCGCAACCAGGCCGCCGGCTGCGCCAACTTCACCACCATCCAGAAGGCGGT
GGACGCGGTGCCCGACTACGCCGCCACACGCACGCTCGTCGCCGTGGACTCCGGCATCTACAGGGAGAAGGTGGTGTTGT
GGTCCAACAAGACGGCCCTCACGCTGCACGGCCGCGGCAACCTCAACACCACCGTCGCCTGGAACGCCACCTCCAACTCC
ACCGGCGGCAGCACCGTGTACAGCGCCACCTTCTCCGTCCTCGCCCCCGCCTTCGTCGCCTACAACATCACCTTCCAGAA
CACGTCGCCCCCGCCCGAGCCCGGGGACGCAGGGGGGCAGGCGGTGGCGCTGAGGGTGGCCGGCGACGAGGCGGCGTTCC
ACTGGTGCGGGGTGTACAGCGCGCAGGACACGCTGCTGGACGAGTCCGGGCGGCACCTGTTCCGCGGCTGCTACATCGAG
GGCTCCATCGACTTCATCTTCGGCAACGCACGATCCCTCTACGTGGGTTGCACCATAAGCTCCGTGGCCATGGCGAGCGC
GACGGGGAATAAGGAAGTGACGGGGAGCGTGACGGCGCAGGGGAGGGCGTCGGCGGCGGAGAGGACGGGGTTCGCGTTCG
TGCGGTGCAGCGTGGTGGGGACGGGGCAGGTGTGGCTGGGGAGGGCGTGGGGGCCGTACGCGACGGTGGTGTTCGCGGAG
ACGTACCTCGGCGACGTGGTGGCGGCGGAGGGGTGGGACGACTGGGGCGACCCCGGCAGGCGGCAGCAGGTGTGGTTCGC
GGAGTACGCGTGCTGGGGCCCCGGATCCGCCACCGCCGCCACCGGCAGGGTGTCCTACGCGCGGCAGCTTGACCAGCGCC
AGGCCGCGCCCTTCATGGACGTCTCCTACATCGACGCCAACCAGTGGGCGCTGCCACCGTCGACGCCGGAACTCTACGGA
TCGAGATATACTCCCAGCTAG

Alignment

ORF - retro_ogla_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.25 %
• Parental protein coverage: 60.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCCNFTTVQAAVNAVPSFSKKRNVVWINKGIYYEKVTVPATKPNITFQGQGFDLTAISWNDTANSSHG-T
          GC.NFTT.Q.AV.AVP.....R..V....GIY.EKV.....K...T..G.G...T...WN.T.NS..G.T
Retrocopy GCANFTTIQKAVDAVPDYAATRTLVAVDSGIYREKVVLWSNKTALTLHGRGNLNTTVAWNATSNSTGGST

Parental  FYSGSVSVFATGFVAKNISFINVAPIPRPGDVGAQAVALRIGGDQAAFWGCGFFGAQDTLHDDRGRHYFK
          .YS...SV.A..FVA.NI.F.N..P.P.PGD.G.QAVALR..GD.AAF..CG...AQDTL.D..GRH.F.
Retrocopy VYSATFSVLAPAFVAYNITFQNTSPPPEPGDAGGQAVALRVAGDEAAFHWCGVYSAQDTLLDESGRHLFR

Parental  ECFIQGSIDFIFGDARSLYENCRVISIADPVPAGVRTITGSVTAHARESVDDNTGYSFVNCSIGGTGRIW
          .C.I.GSIDFIFG.ARSLY..C...S.A.....G....TGSVTA..R.S....TG..FV.CS..GTG..W
Retrocopy GCYIEGSIDFIFGNARSLYVGCTISSVAMASATGNKEVTGSVTAQGRASAAERTGFAFVRCSVVGTGQVW

Parental  LGRAWRPYSTVVFAYTSMSDIIASEGWNDWNDPSRDQ
          LGRAW.PY.TVVFA.T...D..A.EGW.DW.DP.R.Q
Retrocopy LGRAWGPYATVVFAETYLGDVVAAEGWDDWGDPGRRQ

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_15 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	ORGLA08G0054200	1 retrocopy	retro_ogla_15 ,
Oryza sativa japonica	OS08G0206950	1 retrocopy	retro_osat_13,
Sorghum bicolor	Sb07g006050	1 retrocopy	retro_sbic_44,