RetrogeneDB ID: retro_osat_17

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 2:7770037..7771054(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS02G0237000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS01G0205900
• Aliases: None
• Description: None

Sequence

>retro_osat_17
ATGGCGGCAATGTCTGCTTCGGGCCGGAGGGTCTTCTTGCTCGGTGCCCTTCTGCTCGTCGCCGTCTCCTGCCATGGCGG
CTTTGGCGGCGTCGGCGTGGCGGAGGGTTTGTCGACGAGGTACTATGCTAAGACGTGCCCCGCCGTGGAGTCCGTCGTTC
GGTCGGTGATGGCGCGGGCGGTGGCGGCGGACCGGCGCATGGGCGCGTCCGTGCTCAGGCTCTTCTTCCACGACTGCTTC
GTGAACGGCTGCGACGGGTCCGTCCTGCTCGACGACGCGCCGCCGGGGTTCACCGGGGAGAAGGGCGCCGGCGCGAACGC
CGGCTCCGCGCGCGGGTTCGAGGTGGTGGACGCGGCGAAGGCGCGGGTGGAGGCGGCGTGCCGCGCCACCGTGTCGTGCG
CCGACGTGCTCGCGCTCGCCGCGCGCGACGCCGTGGCGCTCCTCGGCGGGACGACGTGGCCCGTGAGGCTGGGACGGAAG
GACGCCCGCACGGCGAGCCAGGCCGCGGCGAACGGCAACCTCCCCGGTCCGGTGTCAAGCCTCACCTCGCTGCTCGCCAC
GTTCGCCGCCAAGGGCCTTTCGGCGCGCGACATGACGGCGCTGTCGGGCGCGCACACGGTGGGGCGCGCCCGGTGCGCCA
CGTTCCGCGGCCGCGTCAACGGCGGCGACGCCAACGTGAACGCCACCTTCGCCGCCCAGCTCCGGCGCCTGTGCCCCGCG
GGCACCGGCGGCGACGGCAACCTCGCGCCGCTGGACGCCGAGACGCCCGACGTGTTCGACAACGGCTACTTCCGCGAGCT
GACGAAGCAGCGCGGGCTGCTGCACTCGGACCAGGAGCTGTTCGCCGCCGGCGGCGGCGGCAGGTCGTCGTCGCAGGACG
CGCTGGTGCGGAAGTACGCCGGCAACGGGGCGAAGTTCGCGAGGGACTTCGCCAAGGCGATGGTGAAGATGGGGAACCTC
GCGCCGGCCGCCGGGACGCCGGTGGAGGTCAGGCTCAACTGCCGGAAGCCCAACTAG

Alignment

ORF - retro_osat_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.91 %
• Parental protein coverage: 91.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSPGYYNATCPGVVSIVRRGMAQAVQKESRMGASILRLFFHDCFVNGCDASILLDDTA-NFTGEKNAGPN
          LS..YY..TCP.V.S.VR..MA.AV....RMGAS.LRLFFHDCFVNGCD.S.LLDD....FTGEK.AG.N
Retrocopy LSTRYYAKTCPAVESVVRSVMARAVAADRRMGASVLRLFFHDCFVNGCDGSVLLDDAPPGFTGEKGAGAN

Parental  ANSVRGYEVIDAIKAQLEASCKATVSCADIITLAARDAVNLLGGPNWTVPLGRRDARTTSQSAANTNLPP
          A.S.RG.EV.DA.KA..EA.C.ATVSCAD...LAARDAV.LLGG..W.V.LGR.DART.SQ.AAN.NLP.
Retrocopy AGSARGFEVVDAAKARVEAACRATVSCADVLALAARDAVALLGGTTWPVRLGRKDARTASQAAANGNLPG

Parental  PGASLASLLSMFSAKGLDARDLTALSGAHTVGWARCSTFRTHIY-NDTGVNATFASQLRTKSCPTTGGDG
          P..SL.SLL..F.AKGL.ARD.TALSGAHTVG.ARC.TFR......D..VNATFA.QLR......TGGDG
Retrocopy PVSSLTSLLATFAAKGLSARDMTALSGAHTVGRARCATFRGRVNGGDANVNATFAAQLRRLCPAGTGGDG

Parental  NLAPLELQAPNTFDNAYFTDLLSRRVLLRSDQELFGSGAG--NGTTDAFVRAYAANATTFAADFAAAMVR
          NLAPL....P..FDN.YF..L...R.LL.SDQELF..G.G......DA.VR.YA.N...FA.DFA.AMV.
Retrocopy NLAPLDAETPDVFDNGYFRELTKQRGLLHSDQELFAAGGGGRSSSQDALVRKYAGNGAKFARDFAKAMVK

Parental  LGNLSPLTGKNGEVRINCRRVN
          .GNL.P..G...EVR.NCR..N
Retrocopy MGNLAPAAGTPVEVRLNCRKPN

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

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

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_17 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa japonica 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 japonica	OS01G0205900	1 retrocopy	retro_osat_17 ,
Oryza sativa japonica	OS01G0543100	1 retrocopy	retro_osat_3,