RetrogeneDB ID: retro_omer_14

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 1:26837356..26838376(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI01G25480
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI08G04560
• Aliases: None
• Description: None

Sequence

>retro_omer_14
ATGGCTCGCGATTTTACGGCAACGTTTCTTCTGCTGCTCAGCGTCGCGTCGCTGCTGGTGATCTCGCCGTGCGCGGCCCA
GCAGATCAAGACCACCGACACGCGGTGGAGCTACCACCTCCCGCTTCCCGACGGCGTCAGCGGCGCCGAGAGCCTCGCCT
TCGACGGCAAGGACGGCCTCTACACCGGCGTCTCGGACGGCCGCGTGCTCAAGTGGGGTGGCAGCGCCGCCGGCTGGACC
ACGTTCGCGTATAATGCGAACTACCGGAAAATCCCTCTGTGCTCGTCGTCCGAGGTGCCACCGGAGGAGAGGGAGAGCAT
CTGCGGGCGCCCGCTGGGGATCCGGTTGTTCAGGAAGACCGGCGAGCTCTACATCGCCGACGCGTACAAGGGGCTGATGA
AGGTCGGGCCCGACGGCGGCGAGGCCCAGGCGGTCGCGACCGAGGCGGACGGCGTCCCCTTCCACTTCCTCAATGGCCTT
GACGTCGACCAAGCCACGGGTGACGCCTACTTCACCGACAGCAGCAGCACGTACACCCGCAGGTTCAACGGCGAGATCAC
GATGAACGCCGACGCGACAGGGCGGCTGCTCAAGTACGACGCGCGGACGCGGCGGGTCACCGTGCTGAAGGCCGACCTGC
CGTACCCGAACGGCGTCGCCGTCAGCCGAGACAGGACGCACCTCGTCGTGGCGCACACCGTGCCGTGCCAGGCGTTCCGG
TACTGGCTGCGCGGCACCAAAGCCGGCGAGTACGAGCTCTTCGCCGACCTCCCGGGCTACCCCGACAACGTGAGGCGCGA
CACCAAGGGAGGCTACTGGGTAGCGCTCAACCAGGAGAGGATGCGGTTGGGCGCCGCGCCCGCGGCCAAGCACCTGGTCG
GCGTACGGCTCAACCCCGACGGCGTGGAGGTGGAGGAGTTGACGGCTGCCAAGGGCGTCACGCTCAGCGAGGTGGCGGAG
CAGAAGGGCAAGCTGTGGTTGGGCTCCGTCGAACTCGATTACATTGGCATGTTTGCTTGA

Alignment

ORF - retro_omer_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 92.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAATPCAAQQVKTSHAQFAFHLPLPDGVTGAESLAFDSSNHGPYTGVSDGRVLRWGGAATGWTTFAHHEN
          L...PCAAQQ.KT.......HLPLPDGV.GAESLAFD....G.YTGVSDGRVL.WGG.A.GWTTFA...N
Retrocopy LVISPCAAQQIKTTDTRWSYHLPLPDGVSGAESLAFDGKD-GLYTGVSDGRVLKWGGSAAGWTTFAYNAN

Parental  YRKIPMCTTPVAPAEETESMCGRPLGLAFHDMTGDLYIADAYKGLMRVGPRGGEAKVLAAGADGVPFNFL
          YRKIP.C.....P.EE.ES.CGRPLG......TG.LYIADAYKGLM.VGP.GGEA...A..ADGVPF.FL
Retrocopy YRKIPLCSSSEVPPEERESICGRPLGIRLFRKTGELYIADAYKGLMKVGPDGGEAQAVATEADGVPFHFL

Parental  NGIDVDQATGDVYFTDSSTTYPRRFNSEIMMNADATARLLKYDAATKRVTVLRAGLPYANGVAVSRDGSH
          NG.DVDQATGD.YFTDSS.TY.RRFN.EI.MNADAT.RLLKYDA.T.RVTVL.A.LPY.NGVAVSRD..H
Retrocopy NGLDVDQATGDAYFTDSSSTYTRRFNGEITMNADATGRLLKYDARTRRVTVLKADLPYPNGVAVSRDRTH

Parental  AVVAHTVPCQAFRYWIKGPNAGEYELLADLPGYPDNVRRDARGGYWVALNQEKVRLDAAAAAAPPAKHLV
          .VVAHTVPCQAFRYW..G..AGEYEL.ADLPGYPDNVRRD..GGYWVALNQE..RL.AA....P.AKHLV
Retrocopy LVVAHTVPCQAFRYWLRGTKAGEYELFADLPGYPDNVRRDTKGGYWVALNQERMRLGAA----PAAKHLV

Parental  GVRLDGDGVEVEELTAAKGVTLSEVVEKGGKLWLGSVELDFIGL
          GVRL..DGVEVEELTAAKGVTLSEV.E..GKLWLGSVELD.IG.
Retrocopy GVRLNPDGVEVEELTAAKGVTLSEVAEQKGKLWLGSVELDYIGM

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_14 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA028079	1 retrocopy	retro_oind_6,
Oryza glumaepatula	OGLUM08G04830	1 retrocopy	retro_oglu_15,
Oryza meridionalis	OMERI08G04560	1 retrocopy	retro_omer_14 ,
Oryza punctata	OPUNC08G04420	1 retrocopy	retro_opun_39,
Oryza glaberrima	ORGLA08G0040000	1 retrocopy	retro_ogla_41,
Oryza rufipogon	ORUFI08G05030	1 retrocopy	retro_oruf_9,
Oryza sativa japonica	OS08G0175000	1 retrocopy	retro_osat_11,