RetrogeneDB ID: retro_omer_25

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 5:11785410..11786259(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI05G09410
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI03G37300
• Aliases: None
• Description: None

Sequence

>retro_omer_25
ATGGCCGGCGGCGGGCAGGCGGCGGCGTCGCTGCTGACGAAGCTGGCGCAAGCGGCGGCCGGGCTGGGCATCGCGGCGTC
GGCGGCGTCGACGGCGCTGTATACGGTGGACGGCGGGCAGCGCGCCGTAATCTTCGACCGGTTCCGCGGCGTGCTCCCGG
AGACCTCGTCGGAGGGCACCCACTTCATCGTCCCCTGGCTCCAGAAGCCCTTCATCTTCGACATCCGCACCCGCCCGCAC
AGCTTCTCCTCCACCTCCGGGACCAAGGACCTACAGATGGTCAGCCTCACCCTCCGCGTCCTCGCGCGCCCCGACGTCGA
CCGCCTCCCGGACATCTTCACCTCGCTGGGCCTCGAGTACGACGAGAAGGTGCTCCCCTCCATCGGCAACGAGGTGCTCA
AGGCCGTCGTCGCGCAGTTCAACGCCGACCAGCTCCTCACCGAGCGCCCCCACGTCTCCGCGCTCGTCCGCGACTCCCTC
ATCCGCCGCGCCGCCGAGTTCAACATCGTCCTCGACGACGTCGCCATCACGCACCTCGCCTACGGCCCGGAGTTCTCCCA
GGCTGTCGAGAAGAAGCAGGTGGCGCAGCAGGAGGCCGAGCGGTCCAGGTTCCTCGTCGCGCGCGCCGAGCAGGAGAGGC
GCGCCGCCATCGTCCGCGCCGAGGGGGAGAGCGAGGCCGCGCGGCTCATCTCCGAGGCCACCGCCGCCGCGGGCACCGGC
CTGATCGAGCTCAGGAGGATCGAGGCCGCCAAGGAGATCGCCGGGGAGCTTGCGCGCTCCCCCAATGTCTCGTACATCCC
GGCCGGCGATAGCAGCCAGATGCTGCTTGGTCTTAGCGGCGCTCGGTGA

Alignment

ORF - retro_omer_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.95 %
• Parental protein coverage: 86.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAAIYAAFNSLYNVEGGHRAIVFNRLEGIKDKVYPEGTHFMIPWFERPIIYDVRARPNLVESTSGSRDLQ
          G.A..AA...LY.V.GG.RA..F.R..G.......EGTHF..PW...P.I.D.R.RP....STSG..DLQ
Retrocopy GIAASAASTALYTVDGGQRAVIFDRFRGVLPETSSEGTHFIVPWLQKPFIFDIRTRPHSFSSTSGTKDLQ

Parental  MVRIGLRVLTRPLPEKLPTIYRSLGENFNERVLPSIIHETLKAVVAQYNASQLITQREAVSREIRKILTE
          MV...LRVL.RP....LP.I..SLG....E.VLPSI..E.LKAVVAQ.NA.QL.T.R..VS...R..L..
Retrocopy MVSLTLRVLARPDVDRLPDIFTSLGLEYDEKVLPSIGNEVLKAVVAQFNADQLLTERPHVSALVRDSLIR

Parental  RASNFNIALDDVSITSLSFGKEFTHAIEAKQVAAQEAERAKFIVEKAEQDKRSAIIRAQGEAKSAQLIGE
          RA..FNI.LDDV.IT.L..G.EF..A.E.KQVA.QEAER..F.V..AEQ..R.AI.RA.GE...A.LI.E
Retrocopy RAAEFNIVLDDVAITHLAYGPEFSQAVEKKQVAQQEAERSRFLVARAEQERRAAIVRAEGESEAARLISE

Parental  A-INNNPAFLALRQIEAAREISHTMASSNNKVYL---DSKDLLLGL
          A..........LR.IEAA.EI....A.S.N..Y....DS...LLGL
Retrocopy ATAAAGTGLIELRRIEAAKEIAGELARSPNVSYIPAGDSSQMLLGL

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_25 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza meridionalis	OMERI03G37300	1 retrocopy	retro_omer_25 ,
Prunus persica	PRUPE_ppa009505mg	1 retrocopy	retro_pper_51,
Vitis vinifera	VIT_19s0085g00730	1 retrocopy	retro_vvin_19,