RetrogeneDB ID: retro_ogla_16

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 10:293799..295524(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA10G0002200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA07G0020300
• Aliases: None
• Description: None

Sequence

>retro_ogla_16
ATGGCAGCCTCGCCGGAGTCGTCTCCGTCGTCGGCCAACTCCACCACCCCGTCAGCACCGTCGCCGTCTTCGTCGTTGTC
AAAATCACCCTCACCTCCCTCCCCATCATCGCCGCCGCCACCAGCATCGACGAACGCGCCACCAAAATCAGCTGGCGGCG
TTTCATCTTCCACGCAAGCGCAACCATCGTCGGAATCATCGTCGGAGTCTACGACTACGCCTTCGGCGCCAGCGGAGAGG
AAGAGCGGCGGGTCCTCTCGAGGAGAGTCCGGGCGGTCGTCGGAGCACATCATCGATCGCGGTGATGTGACCGCCGGCGT
GTTTGTGGGATTGTTTGTGGTGGCGATGGTTGCGGTGTTGGCGGGTGTGGTGGCCATCGTGGTGTGCTGCTGTATAAAGA
TGACGAAGAAGAAGAAGCGGCCGCCGCCGCCGAACATGCCCTTCTTCACCGACGAGAAGGGCAACGTGTACTACGCCACA
GGCGGCCTGCCTCCCATGTGGCAGCAGCATGGCAGCAGCAACTACAGCATCCCACCTCCGCCGCCGCCCGGCTGGCACAT
GTCATCGTCGGCGGGGGGTTTCAGCGGCGAGATGGGGATGGGGTACTCGTCGGGACCGTACGGTCCGGCGCTGCCGCCGC
CGTCGCCGAACGTGGCGCTGGGTTTCTCCAAGAGCTCCTTCTCGTACGAGGAGCTGGCGGCGGCGACGTCGGGGTTCTCG
GCGGCGAACCTGCTGGGGCAGGGAGGGTTCGGGTACGTGTACAAGGGGGTGCTCGCCGGGAGCGGGAAGGAGGTGGCGGT
GAAGCAGCTCAAGTCCGGGAGCGGGCAGGGGGAGCGGGAGTTCCAGGCGGAGGTGGACATCATCAGCCGCGTCCACCACC
GCCACCTCGTGTCTCTGGTGGGATACTGCATCGCCGCCAACCAGCGCATGCTCGTCTACGAGTACGTCCCCAACGGCACC
CTCGAGCACCACCTCTATAGAGGCGGCAATGGCGATCGAGTTCTAGACTGGTCGGCGCGGCACAGGATCGCGCTGGGGTC
GGCCAAGGGTCTCGCCTACCTCCACGAAGACTGCCACCCGCGGATCATCCACCGCGACATCAAGGCGGCCAACATCCTCC
TGGACGCCAACTACGAGGCCATGGTCGCCGACTTCGGCCTCGCCAAGCTCACCACCGACACCAACACCCACGTCTCCACC
CGCGTCATGGGCACCTTCGGCTACCTGGCCCCCGAGTACGCCTCCACCGGCAAGCTCACCGAGAAGTCCGACGTCTTCTC
CTTCGGCGTCATGCTGCTGGAGCTCCTCACCGGGCGGCGGCCCGTCGACACCTCCAACTACATGGAGGACAGCCTCGTGG
ACTGGGCGAGGCCGGTGCTGGCGCGCTTGCTGGCCGCCGGCGGCGAGGAAGGAGGATTAATCCGGGAGCTGGTGGACTCG
CGGCTGGGCGGGGAGTACTCGGCGGTGGAGGTGGAGAGGATGGCGGCGTGCGCGGCGGCGAGCATCCGGCACTCGGCGCG
GCAGCGGCCCAAGATGAGCCAGATCGTGAGGGCGCTGGAGGGGGACGCCTCGCTCTCGCTGGACCACCACCACGACGACG
ACTTCTCCGCCTCATCGGAGATCTCGCGGCATCGGCAGGTGGCCTTCGACAGCGGCGACTACACCGACGACTACTCCACC
ACCTCCACCTCCACCCACTCCTCCCGCCTCCCACCCAAGCGCTAA

Alignment

ORF - retro_ogla_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.3 %
• Parental protein coverage: 60.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLVPPPPPPVPAGLDENAFGYDELAAATGGFSEGNMLGQGGFGYVYRGVL-GDGKEVAVKQLSTGGGQGE
          P..PPP.P.V..G.....F.Y.ELAAAT.GFS..N.LGQGGFGYVY.GVL.G.GKEVAVKQL..G.GQGE
Retrocopy PALPPPSPNVALGFSKSSFSYEELAAATSGFSAANLLGQGGFGYVYKGVLAGSGKEVAVKQLKSGSGQGE

Parental  REFQAEVDMISRVHHRHLVPLVGYCIAGTQRLLVYDFVPNRTLEHHLHE--KGLPVMKWTTRLLIAVGSA
          REFQAEVD.ISRVHHRHLV.LVGYCIA..QR.LVY..VPN.TLEHHL.....G..V..W..R..IA.GSA
Retrocopy REFQAEVDIISRVHHRHLVSLVGYCIAANQRMLVYEYVPNGTLEHHLYRGGNGDRVLDWSARHRIALGSA

Parental  KGLAYLHEECNPRIIHRDIKSANILLDNNFEPLVADFGMAKLTSENVTHVSTRVMGTFGYLAPEYASSGK
          KGLAYLHE.C.PRIIHRDIK.ANILLD.N.E..VADFG.AKLT....THVSTRVMGTFGYLAPEYAS.GK
Retrocopy KGLAYLHEDCHPRIIHRDIKAANILLDANYEAMVADFGLAKLTTDTNTHVSTRVMGTFGYLAPEYASTGK

Parental  LTDKSDVFSYGVMLLELLTGRRPADRSSYGADCLVDWARQALPRAMAGVG--GGGYDDIVDSRLRGDYDR
          LT.KSDVFS.GVMLLELLTGRRP.D.S.Y..D.LVDWAR..L.R..A..G..GG.....VDSRL.G.Y..
Retrocopy LTEKSDVFSFGVMLLELLTGRRPVDTSNYMEDSLVDWARPVLARLLAAGGEEGGLIRELVDSRLGGEYSA

Parental  AEAARVAACAAACVRHAGRRRPKMSQVVKVLEGDVS
          .E..R.AACAAA..RH..R.RPKMSQ.V..LEGD.S
Retrocopy VEVERMAACAAASIRHSARQRPKMSQIVRALEGDAS

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_16 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 glumaepatula	OGLUM07G14400	1 retrocopy	retro_oglu_23,
Oryza glaberrima	ORGLA07G0020300	1 retrocopy	retro_ogla_16 ,
Oryza rufipogon	ORUFI07G02180	1 retrocopy	retro_oruf_34,