RetrogeneDB ID: retro_opun_11

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 6:1835841..1837149(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC06G02690
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC06G17690
• Aliases: None
• Description: None

Sequence

>retro_opun_11
ATGGCGGGCTCCGTCACGGGGAGCCGCCGCCTCTGCATTCTCTTCTACGTCCTCGCCGTCGTCGTCGTCGTGGTCACCGC
GGCGCACAACGCCACCGTCGACGAGGAGTACTGGGAGAAGCGCGCCGAGGAGGCCCGCTCGTTCAACCGCGCCGCCTACG
TGAGCGACCCCGTCGCCACCCTGAACAGCTTCAACGCCGACGTGCTCCGCGCCACCACGCGGCGGTCGCTGGCCAAGTAC
ACGGGCCCATGCATGGCGACCAACCCCATCGACCGTTGCTGGCGCTGCCGCGGCGACTGGGCCACCGACCGGAAGCGTCT
GGCGCAGTGCGTCCGCGGGTTCGGCCACAGGACCGTCGGCGGCGCCGCCGGCAAGATCTACGTGGTGACCGACGCCAGCG
ACGACGAGATGATCATGCCGAGGAAAGGGACGCTCCGGTACGGCGTGATCCAGGACCGGCCGATGTGGATCGTGTTCGCG
CGCGACATGATCATCCAGCTCCGGCAAGAGCTGATCGTGAACCACAACAAGACCATCGACGGCCGCGGCGCGCAGGTGCA
CATCACCGGCGCCCAGATCACGCTCCAGGGCGTCCAGCACGTGATCATCCACAACGTCCACATCCACCACTCGGCGCAGC
ACGGCGGCGGCATGATCCGCGACTCCAAGCACCACTACGGCCTCCGCACGCGCAGCGACGGCGACGGCATCTCCATCATG
TCATCCAGCAACATCTGGATCGACCACGTCTCCATGTCCAACTGCTCCGACGGCCTCATCGACGCCGTCAACGGCTCAAC
CGCCATCACCATCTCCAACGGCCACTTCACCAAGCACGACCACGTCATGCTGTTCGGCGCCAGCAACGGCGACGCGCAGG
ACGCGGTGATGCAGGTCACCGTGGCGTTCAACCACTTCGGCAAGGGGCTCGTGCAGCGGATGCCGCGGTGCAGGTTCGGC
TTCTTCCACGTCGTGAACAACGACTACACGCACTGGCTCATGTACGCCATCGGCGGCAACATGAACCCCACCATCATCAG
CCAGGGGAACAGGTTCATCGCGCCCAACGACGTCAACGCCAAGGAGGTGACCAAGAGGGAGTACACGCCGTACGACGAGT
ACAAGGAGTGGGTGTGGAAGTCGCAGGGGGACGTGATGATGAACGGCGCCTTCTTCAACGAGTCCGGCGGCCAGAACGAG
CGCAACTACGACCAGCTCGACTTCATCCCTGCCAAGCACGGCAAGTACGTCGGCCAGCTCACCCAGTTCGCCGGCGCGCT
CAACTGCCGCGTCGGCATGCCATGCTAG

Alignment

ORF - retro_opun_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.52 %
• Parental protein coverage: 90.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLADAAAEATYKRDPFEVTDTFNRAVHRHVIAAVIRSVAESEEESGRRELAMTKRKKFAGPCKATNPIDR
          ....AA..AT......E......R...R............S......R........K..GPC.ATNPIDR
Retrocopy VVVTAAHNATVDEEYWEKRAEEARSFNRAAYVSDPVATLNSFNADVLRATTRRSLAKYTGPCMATNPIDR

Parental  CWRCRNDWATDRKRLARCAQGFGRNTTGGMAGKFYLVTDGTDDDVLNPRPGTLRWGVIQDEPLWIIFAKD
          CWRCR.DWATDRKRLA.C..GFG..T.GG.AGK.Y.VTD..DD....PR.GTLR.GVIQD.P.WI.FA.D
Retrocopy CWRCRGDWATDRKRLAQCVRGFGHRTVGGAAGKIYVVTDASDDEMIMPRKGTLRYGVIQDRPMWIVFARD

Parental  MIINLKEEMMINNDKTIDGRGAQVRITNGAQVTVQHSNNVIIHNIHIHDIVLGKGGMIRDSPEHFGFRTQ
          MII.L..E...N..KTIDGRGAQV.IT.GAQ.T.Q....VIIHN.HIH......GGMIRDS..H.G.RT.
Retrocopy MIIQLRQELIVNHNKTIDGRGAQVHIT-GAQITLQGVQHVIIHNVHIHHSAQHGGGMIRDSKHHYGLRTR

Parental  SDGDGITIFGSTNVWLDHLSLSNCQDGLIDVIAKSTGVTISNCHLTNHNDVMLFGSSDSYTEDQIMQITV
          SDGDGI.I..S.N.W.DH.S.SNC.DGLID....ST..TISN.H.T.H..VMLFG.S.....D..MQ.TV
Retrocopy SDGDGISIMSSSNIWIDHVSMSNCSDGLIDAVNGSTAITISNGHFTKHDHVMLFGASNGDAQDAVMQVTV

Parental  AFNHFGRGLVQRMPRCRWGFFHVVNNDYTHWLMYAIGGSKNPTIISQGNRYIAPPNLAAKQITKQLGAAE
          AFNHFG.GLVQRMPRCR.GFFHVVNNDYTHWLMYAIGG..NPTIISQGNR.IAP....AK..TK......
Retrocopy AFNHFGKGLVQRMPRCRFGFFHVVNNDYTHWLMYAIGGNMNPTIISQGNRFIAPNDVNAKEVTKREYTPY

Parental  SEWKNWVWHSEEDLFMEGAYFTTSGGAIQRQFSNKDLIKPKPGSYVTRLTRFAGSIPCTPGKPC
          .E.K.WVW.S..D..M.GA.F..SGG...R.....D.I..K.G.YV..LT.FAG...C..G.PC
Retrocopy DEYKEWVWKSQGDVMMNGAFFNESGGQNERNYDQLDFIPAKHGKYVGQLTQFAGALNCRVGMPC

Legend:

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

Expression

RNA-Seq

Oryza punctata was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_11 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC01G35260	1 retrocopy	retro_opun_9,
Oryza punctata	OPUNC06G17690	1 retrocopy	retro_opun_11 ,
Setaria italica	Si006418m.g	1 retrocopy	retro_sita_6,