RetrogeneDB ID: retro_oind_25

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 3:275619..276768(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA011643
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA020885
• Aliases: None
• Description: None

Sequence

>retro_oind_25
ATGGCCTTCTTCGTCAAGATTTCGGCGCCGTGCTCGCTTGCCGGCCATGGCACCACCAGCAGTAGCAGTGGCAGCAGCAG
GTCAAAGAGGGGATTGTTGCTTCCAGTTGGGGCTGGGGCTGGGGCTGGGGCCTACGGCGGCAGGCAGTACTCGGACGTGG
TCCCGGTGCCAGCGCTATCGCAGGCGCAGGCGAGCTCTAGCGGTGGTCGGCTGCGCATCTTCTCCGGCACGGCGAACCCG
AGGCTGGCGCAGGAGGTGGCGTGCTACCTGGGGATGGAGCTGGGGAGGGTGAAGATCAAGCGGTTCGCGGACGGGGAGCT
GTACGTGCAGCTGCAGGAGAGCGTGCGTGGGTGCGACGTGTTCCTGGTGCAGCCCACCTGCCCGCCGGCAAACGAGAACC
TGATGGAGCTCCTCATCATGATCGACGCATGCCGCCGCGCCTCCGCCAAGACCATCACCGCCGTCGTGCCCTACTTCGGG
TACGCCCGCGCCGACCGCAAGATGCGCGGCGGCCGGGAGTCGATCGCCGCCAAGCTGGTGGCCAACCTCATCACGGAGGC
CGGCGCCCACCGCGTGCTGGCCTGCGACCTCCACTCGGGGCAGTCCATCGGCTACTTCGACATCCCCGTGGACCATGTGT
ACGGGCAGCCGGTGATCCTGGACTACCTGGCCAGCAAGACCATCTGCCCCGACGAGGTGGTGGTGGTGTCCCCGGACGTG
GGTGGCGTCGCCCGGGCCCGCACCTTCGCCAAGAAGCTGTCGGACGCGCCGCTGGCCATCGTGGACAAGCGGCGGCAGGG
GCACAACCAGTCGGAGGTGGTGCACCTCATCGGCGACGTCAGGGGGAAGGTGGCGGTGATGGTGGACGACATGATCGACA
CTGCGGGGACAGTGTCCCAGGGAGCGGAGCTGCTGCACAGGGAGGGCGCCAGGGCCGTCTACGCCTGCAGCACCCACGCC
GTGCTCAACCCGCCCGCCGTCGACAGGCTCTCCAGCGGCCTCTTCCAGGAGGTGATCGTCACCAACACCGTCCCCGTGCT
TCACCACCGGACCTTCCCCCAGCTCACCGTCCTCTCCGTCGCCAATCTCCTCGGCGAGACCATCTGGCGCGTTCACGACG
ACTGCTCTGTCAGTAGCATCTTCCAGTGA

Alignment

ORF - retro_oind_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 80.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAALRTDGRDSRLKIFSGTANRPLAQEIASYLGVDLGKVLIKRFADGEIYVQLQESVRGCDVFLVQPTCS
          L..........RL.IFSGTAN..LAQE.A.YLG..LG.V.IKRFADGE.YVQLQESVRGCDVFLVQPTC.
Retrocopy LSQAQASSSGGRLRIFSGTANPRLAQEVACYLGMELGRVKIKRFADGELYVQLQESVRGCDVFLVQPTCP

Parental  PVNENLMELFVMIDACRRASARSITVVIPYFGYARADRKAQG-REAITAKLSANLLTEAGSDRVIVCDIH
          P.NENLMEL..MIDACRRASA..IT.V.PYFGYARADRK..G.RE.I.AKL.ANL.TEAG..RV..CD.H
Retrocopy PANENLMELLIMIDACRRASAKTITAVVPYFGYARADRKMRGGRESIAAKLVANLITEAGAHRVLACDLH

Parental  STQALGYFDIPVDHIHGQPVILDYLASKTISKD-LVVVSPDVGGVVRARAFAKKLSDAPLAIVDKRRQGH
          S.Q..GYFDIPVDH..GQPVILDYLASKTI..D..VVVSPDVGGV.RAR.FAKKLSDAPLAIVDKRRQGH
Retrocopy SGQSIGYFDIPVDHVYGQPVILDYLASKTICPDEVVVVSPDVGGVARARTFAKKLSDAPLAIVDKRRQGH

Parental  NMSEVMHLIGDVKGKVAIMVDDMIDTAGTITSAAALLKQEGAEAVYACSTHAVFSPPAIERLSGGIFEEV
          N.SEV.HLIGDV.GKVA.MVDDMIDTAGT....A.LL..EGA.AVYACSTHAV..PPA..RLS.G.F.EV
Retrocopy NQSEVVHLIGDVRGKVAVMVDDMIDTAGTVSQGAELLHREGARAVYACSTHAVLNPPAVDRLSSGLFQEV

Parental  IVTNSILLPEHKCFPQLTVLSMANLVAETIWHVHRDGSVSSIFQ
          IVTN......H..FPQLTVLS.ANL..ETIW.VH.D.SVSSIFQ
Retrocopy IVTNTVPVLHHRTFPQLTVLSVANLLGETIWRVHDDCSVSSIFQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_25 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA020885	1 retrocopy	retro_oind_25 ,
Aegilops tauschii	F775_28569	1 retrocopy	retro_atau_39,