RetrogeneDB ID: retro_omer_16

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 3:16885122..16886214(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI03G18090
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI05G16600
• Aliases: None
• Description: None

Sequence

>retro_omer_16
ATGGCGGAGGTGTGCTGTGATTCTGCGGTGGTGGTCGGGGCGGAGGCGGAGGCGAGGGCGAGGGCGCGCGCGGGGAGGCG
GCGGCGGGCGGGAGTGGAGGGGGCAGGGAGGTGGAACGCGACGGCGGCGACTGCGGCCGCGGCGGCGGGTGTGGGGGTGG
AGGAGGCCGCGACGAGGAAGCGGAGGGCGAGTGGTGGTGAGGCCGGGTTGGTGGTGGTGGCGAAGCGGCACGGGGCGGCG
TCGGTCGCCGGGAGGAGGAGGGAGATGGAGGACGCCGTGTCGCTGCGCGAGGCGTTCGCCGCGCCCGCGGACGGGGAGGT
TGCGGCGGCGAGGTGTGACTTCTATGGGGTGTTCGACGGGCACGGCTGCTCGCACGTGGCGGACGCGTGCAGGGAGCGGA
TGCACGAGCTCGTCGCGGAGGAGATGGGCGCCGGGTCACCGGCGGCGGCGGCGGCGGCGGCGCGCGAGCCGGCGTCTTGG
ACGGGAGTGATGGAGCGGAGCTTCGCGAGGATGGACGCCGAGGTGATCGCCGGCTGCCGAGCCGAGAGCGGCCGCTGCCG
GTGCGAGGGGCAGAAGTGCGACCACGTGGGGTCCACGGCGGTGGTGGCCGTCGTGGAGGAGAGCAGCGTCGTCGTCGCCA
ACTGCGGCGACTCCCGCGCCGTGCTCTGCCGCGGTGGCGCGCCCGTGCAGCTCTCCTCCGACCACAAGCCCGACCGCCCC
GACGAGCTGGAGCGGATCGAGGCGGCCGGCGGCCGCGTCATCTTCTGGGAGGGCGCCCGTGTCCTCGGCGTCCTCGCCAT
GTCGCGCTCCATCGGCGACGCCTACCTGAAGCCCTACGTCACCGCCGTGCCGGAGGTGACGGTGACCGGCAGGTCGGACG
CCGACGAGTGCCTCATCCTCGCCAGCGACGGCCTCTGGGACGTCGTCAGCAACGAGGCCGCGTGCGAGGTGGCGCAGTCG
TGCCTCCGCCGCGGCAGGCAGCGGTGGTGCGCCGAGGCGGCGGCGGTGCTGACCAAGCTGGCCCTCGCTCGCCGCAGCTC
CGACAACATCTCCGTCGTCGTCGTCGATCTCCGGCGAGGCAACGCCTTGTAG

Alignment

ORF - retro_omer_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.17 %
• Parental protein coverage: 59.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYGVTSVCGRRREMEDAVSIRPDFLP---GSTSSGKHHFFGVFDGHGCSHVARMCQDRMHELVVDAYKKA
          R.G..SV.GRRREMEDAVS.R..F.....G........F.GVFDGHGCSHVA..C..RMHELV.......
Retrocopy RHGAASVAGRRREMEDAVSLREAFAAPADGEVAAARCDFYGVFDGHGCSHVADACRERMHELVAEEMGAG

Parental  VSGKEAAAAAP--AWKDVMEKGFARMDDEATSWAKSRTGGEPACRCELQTPARCDHVGSTAVVAVVGPNR
          .....AAAA.....W..VME..FARMD.E.........G....CRCE.Q....CDHVGSTAVVAVV....
Retrocopy SPAAAAAAAREPASWTGVMERSFARMDAEVIAGCRAESG---RCRCEGQ---KCDHVGSTAVVAVVEESS

Parental  VVVANSGDSRAVLCRAGVPVPLSVDHKPDRPDELERIQAAGGRVIYWDGARVLGVLAMSRAIGDGYLKPY
          VVVAN.GDSRAVLCR.G.PV.LS.DHKPDRPDELERI.AAGGRVI.W.GARVLGVLAMSR.IGD.YLKPY
Retrocopy VVVANCGDSRAVLCRGGAPVQLSSDHKPDRPDELERIEAAGGRVIFWEGARVLGVLAMSRSIGDAYLKPY

Parental  VTSEPEVTLTERADDDECLILASDGLWDVVTNEMACEVVRACFR
          VT..PEVT.T.R.D.DECLILASDGLWDVV.NE.ACEV...C.R
Retrocopy VTAVPEVTVTGRSDADECLILASDGLWDVVSNEAACEVAQSCLR

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_16 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA017925	1 retrocopy	retro_oind_21,
Oryza glumaepatula	OGLUM05G20150	1 retrocopy	retro_oglu_4,
Oryza meridionalis	OMERI05G16600	1 retrocopy	retro_omer_16 ,
Oryza nivara	ONIVA05G19940	1 retrocopy	retro_oniv_23,
Oryza glaberrima	ORGLA05G0165000	1 retrocopy	retro_ogla_36,
Oryza rufipogon	ORUFI05G20280	1 retrocopy	retro_oruf_40,