RetrogeneDB ID: retro_omer_9

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 6:31431408..31432275(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI06G27920
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI03G02480
• Aliases: None
• Description: None

Sequence

>retro_omer_9
ATGGAGCAGCAGCAGCGGAGCAGGTCGACAGGAGGAGAGGTGGAGGTGGAGCAGCTGCCGGGATTCAGGTTCCATCCGAC
GGAGGAGGAGCTGCTGGAGTTCTACCTGAAGCAGGTGGTGCAGGGGAAGAAGCTCAAGTTCGACATCATCCCCACCGTCC
ACCTCTACCGCCACGACCCGCGCGAGCTCCCCGGACTCGCCCGCATCGGCGAGCGCGAGTGGTACTTCTTCGTCCCGCGC
GACCGCAAGCAGGCCACCGGCGGCGGCGGTAGGCCCAGCCGCACCACGGAGCGCGGCTTCTGGAAGGCCACCGGCTCCGA
CCGCGCCGTCCGCTGCGCCGCCGACCCCAAGCGCCTCATCGGCCTCAAGAAGACGCTCGTCTACTACGAGGGCCGCGCCC
CTCGCGGCACCAAGACCGACTGGGTCATGAACGAGTACCGCCTCCCCGACGCCATTCCCGACACCATGCAATTGCAAATG
CAACACGACGACATGGTGCTCTGCAAGGTCTACCGGAAGGCGGTCTCCCTCAAGGAGCTGGAGCAGAGGGTCGCCATGGA
GGAGCTTGCACGCTCCACCACCTCCTCCGGCACCCACAACACCGGCTCGCCCCTGCAGCAGGACTCCTCCTCCATCTCCA
TCTCCTCCTCCTCGGACGCCATGAAGAAAGAGGCCGTGGTGGTGGTGGATGAGGCCGCGGCGGCGGCGCATGAGCTGGTC
CGGCCGGCGACGCTGAGCCTGCCGCAGCTGGAGGTGGCGAGGCCGCAGAGCGGGCTGGAGTGGATGCAGGAGCCATTCCT
GACGCAGCTTCGGAGCCCATGGATGGAGACCTGGTCGCCCTACTACGCCAGCGTCCTCAACTTCTGA

Alignment

ORF - retro_omer_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.17 %
• Parental protein coverage: 72.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPSMEVEQDLPGFRFHPTEEELLDFYLSRVVLGKKLQFDIIGTLNIYRHDPWDLPGMAKIGEREWYFFVP
          G...EVEQ.LPGFRFHPTEEELL.FYL..VV.GKKL.FDII.T...YRHDP..LPG.A.IGEREWYFFVP
Retrocopy GGEVEVEQ-LPGFRFHPTEEELLEFYLKQVVQGKKLKFDIIPTVHLYRHDPRELPGLARIGEREWYFFVP

Parental  RDRK--AGNGGRPNRTTERGFWKATGSDRAIRSSGDPKRVIGLKKTLVFYQGRAPRGTKTDWVMNEYRLP
          RDRK...G.GGRP.RTTERGFWKATGSDRA.R...DPKR.IGLKKTLV.Y.GRAPRGTKTDWVMNEYRLP
Retrocopy RDRKQATGGGGRPSRTTERGFWKATGSDRAVRCAADPKRLIGLKKTLVYYEGRAPRGTKTDWVMNEYRLP

Parental  DYGAARAAAPPPKEDMVLCKIYRKATPLKELEQRASAMEEMQRGSSHGDYTATRASLVHDASASTGDDYF
          D.............DMVLCK.YRKA..LKELEQR..AMEE..R.........T...L..D.S........
Retrocopy DAIPDTMQLQMQHDDMVLCKVYRKAVSLKELEQRV-AMEELARSTTSSGTHNTGSPLQQDSSSISISS--

Parental  SSDDVHDSGFLIQSSSSSAA
          SSD...............AA
Retrocopy SSDAMKKEAVVVVDEAAAAA

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_9 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR03G02450	1 retrocopy	retro_lper_29,
Oryza meridionalis	OMERI03G02480	1 retrocopy	retro_omer_9 ,
Oryza punctata	OPUNC03G02420	1 retrocopy	retro_opun_1,