RetrogeneDB ID: retro_oind_28

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 9:17766883..17767876(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA029521
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA016968
• Aliases: None
• Description: None

Sequence

>retro_oind_28
ATGCTTTCCCGGATTCTGCATGGCTATGGAGGACACGGCGGGAGAGGCTTCGAGCAGACGTACCGGTGCTACTCGGCGGC
GGCCTTCAACAAGCCGCAGCTCGAAGGCGGAGACAAGGTGATCATGCCGGCGTCGGCGCTCCACCGCCTCGCCTCCCTCC
ACATCGACTACCCGATGCTGTTCGAGCTCTCCCACCACGGCGACGCCGCCGCCCACCGGGTCACCCACTGCGGCGTGCTG
GAGTTCGTCGCCGACGAGGGCACGGTGATCATGCCGCGGTGGATGATGCGCGGCATGCGCCTCGACGACGGCGGCCTCGT
CGTCGTCAGGAGCGCCAGCCTCCCCAAGGGCAGCTACGCCAAGCTGCAGCCTCACACCGGCGACTTCCTCGACACGGCGA
ACCCCAAGGCCGTCCTGGAGAAGACGCTGCGCAGCTTCACCTGCCTCACCACCGGCGACACCATCATGGTGGCCTACAAC
AACAAGGAGTTCCTCATCGACATCATCGAGACGAAGCCCGCCTCGGCCGTCTGCATCATCGAGACGGATTGCGAGGTCGA
TTTCGCACCTCCACTCGATTACAAAGAACCTGAAAAGGTTCAGCAGAAACCATCTGTTCCTTCAAGCAAGGCGGCTTCCG
AAGATCAAGATCAAATCAAAGATGAGCCAGAATTCAGAGCATTCACTGGTTCAGGGAATCGTTTGGATGGTAAGGCCTCA
AAACCGCTAGCAGCAGGGATCTCTTCTAATCCTGCTGCTGCAAGTTCTGCAATTTCAGACTCGAACAAGAAGGTGAATCA
GGAGACAGCAGCATCAGGAGTTAGCAACTCTACACGTCAGAAAAAGGGGAAGCTTGTTTTTGGTTCAAACAAAAGCAGCA
GCAGCAGCAAAGAACCAGAGAAGGCTCCTCCTGTTAAAGTTGATGAACTTGCAAAGAAGGAAGAGCCCAAGTTCCAAGCA
TTTTCTGGGACGAGCTACTCGTTGAAACGTTAG

Alignment

ORF - retro_oind_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.11 %
• Parental protein coverage: 98.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYGYHGSN-FEQTYRCYPASFFDKPHLEGGDKVIMPPSALDRLASLHIEYPMLFEL--HNDAT-QRISHC
          GYG.HG...FEQTYRCY.A..F.KP.LEGGDKVIMP.SAL.RLASLHI.YPMLFEL..H.DA...R..HC
Retrocopy GYGGHGGRGFEQTYRCYSAAAFNKPQLEGGDKVIMPASALHRLASLHIDYPMLFELSHHGDAAAHRVTHC

Parental  GVLEFVAEEGMIIMPYWMMQNMLLQEGDTVRVKNTTLPKGTYVKLQPHTTDFLDISNPKAILEKTLRNFS
          GVLEFVA.EG..IMP.WMM..M.L..G..V.V....LPKG.Y.KLQPHT.DFLD..NPKA.LEKTLR.F.
Retrocopy GVLEFVADEGTVIMPRWMMRGMRLDDGGLVVVRSASLPKGSYAKLQPHTGDFLDTANPKAVLEKTLRSFT

Parental  CLTTGDSIMVAYNNKQYYIDIVETKPASAVSIIETDCEVDFAPPLDYKEPENPQQ-PSVPASEATAEDEN
          CLTTGD.IMVAYNNK...IDI.ETKPASAV.IIETDCEVDFAPPLDYKEPE..QQ.PSVP.S.A..ED..
Retrocopy CLTTGDTIMVAYNNKEFLIDIIETKPASAVCIIETDCEVDFAPPLDYKEPEKVQQKPSVPSSKAASEDQD

Parental  AKVGDELKFRPFTGSGKRLDGKASKLQATEV---PSASRSSPSDSNKRVNQETLAPASSGASNSTRQKSG
          ....DE..FR.FTGSG.RLDGKASK..A......P.A..S..SDSNK.VNQET...A.SG.SNSTRQK.G
Retrocopy -QIKDEPEFRAFTGSGNRLDGKASKPLAAGISSNPAAASSAISDSNKKVNQET---AASGVSNSTRQKKG

Parental  KLVFGS--SANNNKEPQKA-SVKDDESPKKDEPKFQAFSGKSYSLKR
          KLVFGS..S....KEP.KA..VK.DE..KK.EPKFQAFSG.SYSLKR
Retrocopy KLVFGSNKSSSSSKEPEKAPPVKVDELAKKEEPKFQAFSGTSYSLKR

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_28 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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA016968	1 retrocopy	retro_oind_28 ,
Sorghum bicolor	Sb06g026100	1 retrocopy	retro_sbic_36,