RetrogeneDB ID: retro_opun_21

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:45954272..45955403(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC01G44710
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC05G01050
• Aliases: None
• Description: None

Sequence

>retro_opun_21
ATGGTGCAGCGCACTTCATCCGATTCGACGTCGGCTGCGGCGGAGGCCATGACCATCGACCTCAGTCCTAAGCGCCCCGC
CAAGTTGTACGGCGGCGACGGCGGCGCGTACTATGACTGGTCTCCCTCCGAGCTGCCCATGCTCCGGGCCGCCTCCATCG
GCGCCGCCAAGCTCTCCCTCGCCGCCGGAGGCCTCGCCCTTCCCTCCTACTCCGACTCCGCCAAGGTCGCCTACGTCCTC
CAGGGCAAGGGCACCTGCGCCATCCTCCTTCCGGAGGCGGAGCCCCCGTCCGAGAAGATCCTTCCCATCAAGGAGGGCGA
CGCGCTGGCCCTCCCCTTCGGCGTCGTCACCTGGTGGCACAACCTCCACGCTGCCACCACCGACCTCGTCGTCCTCTTCC
TCGGGGACACCTCCAAGGGGCACACCGCCGGCCGCTTCACCAACATGCAGCTCACCGGCTCCACCGGCATCTTCACCGGC
TTCTCCACCGAGTTCGTCGGCCGCGCATGGGACCTCCCGCAGGACGCCGCCGCCTCGCTCGTGTCCACCCAGGCAGGCGC
CGGCATCGTGAAGGTCAAGGACGGATTCAGGATACCGGAGGGCTCCGACAAGGACAGGGAGGGGATGGTGCTCAACTGCC
TGGAGGCGCCGCTGGACGTGGACATCAAGAACGGGGGGCGCGTGGTGGTGCTCAACACGCAGAACCTGCCGCTGGTGAAG
GAGGTGGGGCTGGGCGCCGACCTGGTGAGGATCGACGGGCACTCCATGTGCTCGCCGGGGTTCTCGTGCGACTCGGCGTA
CCAGGTGACGTACATAGTGCGCGGCAGCGGGCGGGTGCAGGTGGTGGGCATCGACGGGACGCGGGTGCTGGAGACCCGCG
CCGAGGGTGGCTGCCTCTTCATCGTCCCCAGGTTCTTCGTGGTCTCCAAGATCGCCGACGACACCGGCATGGAGTGGTTC
TCCATCATCACCACTCCCAACCCCATCTTCTCCCACCTCGCCGGGAGGACCTCCGTCTGGAAGGCCATCTCCCCCGCCGT
GCTCGAGGCCTCCTTCAACACCACCCCGGAGATGGAGAACCTCTTCCGCTCCAAGAGGCTCGACTCCGAGATCTTCTTCG
CCCCCAACTGA

Alignment

ORF - retro_opun_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.5 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVDLTPRLPRKAYGGDGGTYYEWSPADLAMLEIANIGAAKLSLVAGGFSLPSFSDSGKVAYVLQGKGTCG
          ..DL.P..P.K.YGGDGG.YY.WSP..L.ML..A.IGAAKLSL.AGG..LPS.SDS.KVAYVLQGKGTC.
Retrocopy TIDLSPKRPAKLYGGDGGAYYDWSPSELPMLRAASIGAAKLSLAAGGLALPSYSDSAKVAYVLQGKGTCA

Parental  IVLPEAS--KEKVLAVKEGDALALPFGVVTWWHNLPESTTELVVLFLGDTSKAHKPGQFTNMQLTGATGI
          I.LPEA....EK.L..KEGDALALPFGVVTWWHNL...TT.LVVLFLGDTSK.H..G.FTNMQLTG.TGI
Retrocopy ILLPEAEPPSEKILPIKEGDALALPFGVVTWWHNLHAATTDLVVLFLGDTSKGHTAGRFTNMQLTGSTGI

Parental  FTGFSTEFVGRAWDLAESDAAKLVSSQPASGIVKLKSAQKLPEPSPADREGMALNCLEAPLDVDIKNGGR
          FTGFSTEFVGRAWDL....AA.LVS.Q...GIVK.K.....PE.S..DREGM.LNCLEAPLDVDIKNGGR
Retrocopy FTGFSTEFVGRAWDLPQDAAASLVSTQAGAGIVKVKDGFRIPEGSDKDREGMVLNCLEAPLDVDIKNGGR

Parental  VVVLNTANLPLVKEVGLGADLVRIDGHSMCSPGFSCDSAYQVTYIVRGSGRVQVVGIDGKRVLEARVEAG
          VVVLNT.NLPLVKEVGLGADLVRIDGHSMCSPGFSCDSAYQVTYIVRGSGRVQVVGIDG.RVLE.R.E.G
Retrocopy VVVLNTQNLPLVKEVGLGADLVRIDGHSMCSPGFSCDSAYQVTYIVRGSGRVQVVGIDGTRVLETRAEGG

Parental  NLFIVPRFFVVSKIADASGLQWFSIITTPNPIFSHLAGRTSVWKAISPEVLEVSFNTTPEMEKLFRSKRL
          .LFIVPRFFVVSKIAD..G..WFSIITTPNPIFSHLAGRTSVWKAISP.VLE.SFNTTPEME.LFRSKRL
Retrocopy CLFIVPRFFVVSKIADDTGMEWFSIITTPNPIFSHLAGRTSVWKAISPAVLEASFNTTPEMENLFRSKRL

Parental  DSEIFFAPN
          DSEIFFAPN
Retrocopy DSEIFFAPN

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_21 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA018931	1 retrocopy	retro_oind_1,
Oryza brachyantha	OB05G11140	1 retrocopy	retro_obra_13,
Oryza glumaepatula	OGLUM05G01170	1 retrocopy	retro_oglu_9,
Oryza nivara	ONIVA05G01190	1 retrocopy	retro_oniv_21,
Oryza punctata	OPUNC05G01050	1 retrocopy	retro_opun_21 ,
Oryza glaberrima	ORGLA05G0012000	1 retrocopy	retro_ogla_28,
Oryza rufipogon	ORUFI05G01180	1 retrocopy	retro_oruf_6,
Oryza sativa japonica	OS05G0116000	1 retrocopy	retro_osat_27,