RetrogeneDB ID: retro_omer_21

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 10:114656..116351(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI10G00130
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI01G08000
• Aliases: None
• Description: None

Sequence

>retro_omer_21
ATGGCAGCCTCGCCGGAGTCGTCTCCGTCGGCGGCCAACACCACCACCCCGTCAGCACCGTCGCCGTCTTCGTCGTCGTC
CAAATCACCCTCACCTCCCTCCCCATCATCGCCGCCGCCACCAGCACCGACGAACGCGCCACCAAAATCAGCTGGCGGCG
TTTCTTCTTCCACGCAATCGCAACCATCGTCGGAATCATCGTCGGAGTCTACGACTACGCCTTCGGCGCCAGCGGAGAGG
AAGAGCGGCGGGCCCTCTCGAGGAGAGTCCGGGCGGTCGTCGGAGCACATCATCGATCGCGGTGATGTGACCGCCGGCGT
GTTTGTGGGGTTGTTGGTGGTGGCGATGGTGGCGGTGTTGGCGGGTGTGGTGGCCATCGTGGTGTGCGGCTGTATAAAGA
TGACGAAGAAGAAGAAGCGGCCGCCGCCGCCGCCGCCGCCGAACATGCCCTTCTACACCGACGAGAAGGGCAACGTGTAC
TACCCCACAGGCGGCCTGCCTCCCATGTGGCAGCAGCACGGCAGCAGCAACTACAGCATCCCACCTCCGCCGCCGCCCGG
CTGGCACATGTCGTCGTCGGGTTTCAGCGGCGAGATGTACTCGTCGGGACCGTACGGTCCGGCGCTGCCGCCGCCGTCGC
CGAACGTGGCGCTGGGCTTCTCGAAGAGCTCCTTCTCGTACGAGGAGCTGGCGGCGGCGACGTCGGGGTTCTCGGCGGCG
AACCTGCTGGGGCAGGGAGGGTTCGGGTACGTGTACAAGGGGGTGCTCGCCGGGAGCGGGAAGGAGGTGGCGGTGAAGCA
GCTCAAGTCCGGGAGCGGCCAGGGGGAGCGCGAGTTCCAGGCGGAGGTGGACATCATCAGCCGCGTCCACCACCGCCACC
TCGTGTCCCTCGTCGGATACTGCATCGCCGCCAACCAGCGCATGCTCGTCTACGAGTTCGTCCCCAATGGCACCCTCGAG
CACCACCTCTATAGAGGCGGCAATGGCGATCGAGTTCTAGACTGGTCGGCGCGGCACAGGATCGCGCTGGGGTCGGCCAA
GGGTCTCGCCTACCTCCACGAGGACTGCCACCCGCGGATCATCCACCGCGACATCAAGGCCGCCAACATCCTCCTGGACG
CCAACTACGAGGCCATGGTCGCCGACTTCGGCCTCGCCAAGCTCACCACCGACACCAACACCCACGTCTCCACCCGCGTC
ATGGGCACCTTCGGCTACCTGGCGCCCGAGTACGCCTCCACCGGCAAGCTCACCGACAAGTCCGACGTCTTCTCCTTCGG
CGTCATGCTGCTGGAGCTCCTCACCGGGCGCCGGCCCGTCGACACCTCCAACTACATGGAGGACAGCCTCGTGGACTGGG
CGAGGCCGGTGCTGGCGCGCTTGCTGGCCGCCGGCGGCGAGGAACCCGGATTATTAATCCGGGAGCTAGTGGACTCGCGG
CTGGGCGGGGAGTACTCGGCGGTGGAGGTGGAGAGGATGGCGGCGTGCGCGGCGGCGAGCATCCGGCACTCGGCGCGGCA
GCGGCCCAAGATGAGCCAGATCGTGAGGGCGCTGGAGGGGGACGCCTCGCTCTCGCTCTCGCTGGACCACCACCACCACG
ACGACTTCTCCGCCTCATCGGAGATCTCGCGGCATCGGCAGGTGGCCTTCGACAGCGGCGACTACTCCTCCTCCCGCCTC
TCACCCAAGCGCTAA

Alignment

ORF - retro_omer_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.7 %
• Parental protein coverage: 56.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPPPPAPLNVHSGGSGSNYSGGDNSQ--PLVSPGAALGFSRCTFTYEDLSAATDGFSDANLLGQGGFGYV
          PPPPP......SG.SG..YS.G......P..SP..ALGFS...F.YE.L.AAT.GFS.ANLLGQGGFGYV
Retrocopy PPPPPGWHMSSSGFSGEMYSSGPYGPALPPPSPNVALGFSKSSFSYEELAAATSGFSAANLLGQGGFGYV

Parental  HKGVLP-NGTEVAVKQLRDGSGQGEREFQAEVEIISRVHHKHLVTLVGYCISGGKRLLVYEYVPNNTLEL
          .KGVL...G.EVAVKQL..GSGQGEREFQAEV.IISRVHH.HLV.LVGYCI....R.LVYE.VPN.TLE.
Retrocopy YKGVLAGSGKEVAVKQLKSGSGQGEREFQAEVDIISRVHHRHLVSLVGYCIAANQRMLVYEFVPNGTLEH

Parental  HLH--GRGRPTMEWPTRLRIALGAAKGLAYLHEDCHPKIIHRDIKSANILLDARFEAKVADFGLAKLTSD
          HL...G.G.....W..R.RIALG.AKGLAYLHEDCHP.IIHRDIK.ANILLDA..EA.VADFGLAKLT.D
Retrocopy HLYRGGNGDRVLDWSARHRIALGSAKGLAYLHEDCHPRIIHRDIKAANILLDANYEAMVADFGLAKLTTD

Parental  NNTHVSTRVMGTFGYLAPEYASSGQLTEKSDVFSFGVMLLELITGRRPVRSNQSQMDDSLVDWARPLMMR
          .NTHVSTRVMGTFGYLAPEYAS.G.LT.KSDVFSFGVMLLEL.TGRRPV......M.DSLVDWARP...R
Retrocopy TNTHVSTRVMGTFGYLAPEYASTGKLTDKSDVFSFGVMLLELLTGRRPV-DTSNYMEDSLVDWARPVLAR

Parental  ASDDGNYD--ALVDPRLGQEYNGNEMARMIACAAAC----VRHSARRRPRMSQVVRALEGDVSL
          ....G......L..........G...A......AAC.....RHSAR.RP.MSQ.VRALEGD.SL
Retrocopy LLAAGGEEPGLLIRELVDSRLGGEYSAVEVERMAACAAASIRHSARQRPKMSQIVRALEGDASL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza meridionalis was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza meridionalis was not studied using ChIP-Seq data.

EST

Oryza meridionalis was not studied using EST data.

TSS

Oryza meridionalis was not studied using FANTOM5 data.

Lab

retro_omer_21 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza meridionalis 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 meridionalis	OMERI01G08000	1 retrocopy	retro_omer_21 ,