RetrogeneDB ID: retro_omer_31

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 3:5986769..5987377(-)
• Located in intron of: OMERI03G06880

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI05G21420
• Aliases: None
• Description: None

Sequence

>retro_omer_31
CTCACTGATGCACTAACTTCAGAAAATATTAGCGTATTTCGTTTTGATTTCACTGGCATTGGAGAAAGTGAAGGCGCATT
CCAGTATGGCAACTATTACAAAAAGGTGGATGATTGCGTGATGTAATTCTACATTTCAAGAAACACAAGCGTGACACCCG
CGGTATTGCTGGCCACAGTAAAGGAGGAAATGTGGTCATCCTGTATTCATCCATTCATCGAGATGTAGCTAGTATTATTA
ACATGTCTGGAAGAGTTGATCTAAGACATGGAATTGCTGATCGTCTTGGAAGTGATTATATGGAAAAGATAGACCGGTAT
GGGTTCATTGATGTGGGAGTGAAGACAGGACGTTCCATCTACCGTGTAACCAAAGAAAGTCTGATGGATCGCCTTAAGAT
AGATATGAAGAGTGCATGCATGTCTATTGATCCTAAATGCAGGGTTCTGACAATTCATGGTTCTGATGATGATATTGTGC
CATCAGAGGATGCCTTAGAATTTGACAAATATATAAGCAATCATGAATTGAGTATTATTGAAGGAGCTGATCATAGATAT
TCATTGCATCACCTTGAGTTGGCTACCATTGTACTGAAATTTATTAAG

Alignment

ORF - retro_omer_31 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.41 %
• Parental protein coverage: 77.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAYALTREGISAFRFDFAGNGESEGQFQYGNYRREADD-LHSVVSYFTEQKYNIIGLVGHSKGGNAVLLY
          L..ALT.E.IS.FRFDF.G.GESEG.FQYGNY....DD.L..V...F...K....G..GHSKGGN.V.LY
Retrocopy LTDALTSENISVFRFDFTGIGESEGAFQYGNYYKKVDD<LRDVILHFKKHKRDTRGIAGHSKGGNVVILY

Parental  ASMYHDIPVIVNISGRFALERGIDGRLGKNFMQRINEDGYIDVRNRKGEFEYQVTKESLKDRLSTDTLLS
          .S...D...I.N.SGR..L..GI..RLG...M..I...G.IDV....G...Y.VTKESL.DRL..D....
Retrocopy SSIHRDVASIINMSGRVDLRHGIADRLGSDYMEKIDRYGFIDVGVKTGRSIYRVTKESLMDRLKIDMKSA

Parental  SCSISKGCRVLTIHGSKDEIVPVEDALMFAANIPNHELHIIAEANHRYTGHEKELKALVLDFIK
          ..SI...CRVLTIHGS.D.IVP.EDAL.F...I.NHEL.II..A.HRY..H..EL...VL.FIK
Retrocopy CMSIDPKCRVLTIHGSDDDIVPSEDALEFDKYISNHELSIIEGADHRYSLHHLELATIVLKFIK

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_31 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	OMERI05G21420	1 retrocopy	retro_omer_31 ,