RetrogeneDB ID: retro_opun_20

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 3:22076..23216(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC03G00050
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC02G01640
• Aliases: None
• Description: None

Sequence

>retro_opun_20
ATGGCCTTGTTCGTGAAGATATCGCCGCCGTCATCGTCGTGCTCGCTTGCCGGCCATGGCCATGCGACCAGCAGCAGTAG
CAGGTCAAAGAGGGGATCGTTGCTTCCACTTGGGGCTGGGGCCTACGGCAGGCAGTACTCAGACGTGGTCCCGGTCCCAC
CGGCGCTACCGCAGCCGCAGCCGAGCTCTAGCGGTCGGCTGCGCATCTTCTCCGGCACGGCGAATCCGACGCTGGCGCAG
GAGGTGGCGTGCTACCTGGGCATGGAGCTGGGGCGGGTGAAGATAAAGCGGTTCGCGGACGGGGAGCTGTACGTGCAGCT
GCAGGAGAGCGTGCGTGGGTGCGACGTGTTCCTGGTGCAGCCCACCTGCCCGCCGGCCAACGAGAACCTCATGGAGCTCC
TCATCATGATCGACGCCTGCCGCCGCGCCTCCGCCAAGACCATCACCGCCGTCGTCCCCTACTTCGGCTACGCCCGTGCC
GACCGCAAGATGCGCGGCGGCCGCGAGTCCATCGCCGCCAAGCTCGTCGCCAACCTCATCACGGAGGCCGGCGCCCACCG
CGTACTCGCCTGCGACCTCCACTCCGGCCAGTCCATCGGCTACTTCGACATACCCGTGGACCATGTGTACGGCCAGCCTG
TGATCCTCGACTACCTGGCCAGCAAGACATGCATCTGCCCCGACGAGGTGGTGGTGGTGTCCCCGGACGTGGGTGGCGTC
GCCCGGGCGCGCGCCTTCGCCAAGAAGCTCTCGGACGCGCCGCTGGCCATCGTGGACAAGCGGCGGCAAGGACACAACCA
GTCGGAGGTGGTGCACCTCATCGGCGACGTGAGGGGGAAGGTGGCGGTGATGGTGGACGACATGATCGACACGGCGGGGA
CGGTGTCCCAGGGAGCGGAGCTGCTGCACAGGGAGGGAGCCAGGGCCGTCTACGCCTGCAGCACCCACGCCGTGCTCAGC
CCGCCAGCGGTCGACAGGCTCTCCAGCGGCCTCTTCCAGGAGGTGATTGTCACCAACACCGTCCCCGTGCTTCACCACCG
TACCTTCCCCCAGCTCACCGTCCTCTCCGTCGCCAATCTCCTCGGCGAGACCATCTGGCGCGTTCACGACGACTGCTCTG
TCAGCAGCATCTTCCAGTGA

Alignment

ORF - retro_opun_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.11 %
• Parental protein coverage: 82.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PIIRDANIKNDTRLRIFSGTANPSLSQEIASYLGLELGKINIKRFADGEIYVQLQESVRGCDVFLVQPTC
          P...........RLRIFSGTANP.L.QE.A.YLG.ELG...IKRFADGE.YVQLQESVRGCDVFLVQPTC
Retrocopy PALPQPQPSSSGRLRIFSGTANPTLAQEVACYLGMELGRVKIKRFADGELYVQLQESVRGCDVFLVQPTC

Parental  PPANENLMELLIMIDACRRASAKNITAVIPYFGYARADRKSQ-GRESIAAKLVANMITEAGANRVLVCDL
          PPANENLMELLIMIDACRRASAK.ITAV.PYFGYARADRK...GRESIAAKLVAN.ITEAGA.RVL.CDL
Retrocopy PPANENLMELLIMIDACRRASAKTITAVVPYFGYARADRKMRGGRESIAAKLVANLITEAGAHRVLACDL

Parental  HSSQAMGYFDIPVDHVYGQPVILDYLASKT-ICSDDLVVVSPDVGGVARARAFAKKLSDAPLAIVDKRRH
          HS.Q..GYFDIPVDHVYGQPVILDYLASKT.IC.D..VVVSPDVGGVARARAFAKKLSDAPLAIVDKRR.
Retrocopy HSGQSIGYFDIPVDHVYGQPVILDYLASKTCICPDEVVVVSPDVGGVARARAFAKKLSDAPLAIVDKRRQ

Parental  GHN---VMNLIGDVRGKVAVMMDDMIDTAGTIAKGAELLHQEGAREVYACCTHAVFSPPAIERLSSGLFQ
          GHN...V..LIGDVRGKVAVM.DDMIDTAGT...GAELLH.EGAR.VYAC.THAV.SPPA..RLSSGLFQ
Retrocopy GHNQSEVVHLIGDVRGKVAVMVDDMIDTAGTVSQGAELLHREGARAVYACSTHAVLSPPAVDRLSSGLFQ

Parental  EVIITNTIPLKEDKSFPQLTILSVANLLGETIWRVHDDCSVST
          EVI.TNT.P......FPQLT.LSVANLLGETIWRVHDDCSVS.
Retrocopy EVIVTNTVPVLHHRTFPQLTVLSVANLLGETIWRVHDDCSVSS

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_20 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G02680	1 retrocopy	retro_bdis_29,
Leersia perrieri	LPERR02G02000	1 retrocopy	retro_lper_21,
Oryza brachyantha	OB02G12100	1 retrocopy	retro_obra_24,
Oryza barthii	OBART02G02200	1 retrocopy	retro_obar_2,
Oryza glumaepatula	OGLUM02G02060	1 retrocopy	retro_oglu_34,
Oryza nivara	ONIVA02G02120	1 retrocopy	retro_oniv_9,
Oryza punctata	OPUNC02G01640	1 retrocopy	retro_opun_20 ,
Oryza rufipogon	ORUFI02G02210	1 retrocopy	retro_oruf_33,
Oryza sativa japonica	OS02G0127700	1 retrocopy	retro_osat_35,
Triticum aestivum	Traes_6AS_88F0CBEC0	1 retrocopy	retro_taes_35,