RetrogeneDB ID: retro_opun_7

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:32600728..32601553(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC01G29000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC01G21870
• Aliases: None
• Description: None

Sequence

>retro_opun_7
ATGGCCGGGATCGTGGTGGTGTTCGACTTCGACAAGACGATCATCGACGTCGACAGCGACAACTGGGTGGTCGACGGGCT
CGGCGCAACGGAGGAGTTCGAGAGGCTGCTGCCCACCATGCCGTGGAACACCCTCATGGACACCATGATGGGTGAGCTCC
ACGCGCGCGGGAAGACGCTCGACGACGTCGCGGACGTGCTCAGGTCGGCGCCGCTCGACCCGCGCGTCGTCGCCGCCATC
AAGGCCTGCTACGGCCTCGGCTGCGACCTCCGGATCCTCAGCGATGCCAACCGCTTCTTCATCGACACCATCCTCGACCA
CCACGGCCTCACGGGCTACTTCTCCGAGATCAACACCAACCCGAGCGCCGTCGACGCTGCCACCGGCCGCCTCCGCATCG
CGCCGTACCACGACTTCCACGCCGCGCCGCACGGGTGCGGGCTGGGAATCTGCCCGCCCAACATGTGCAAGGGCCAGGTG
CTCGACCGCATCCGCGCGTCTGCCGCCGCCGCCGCCAAGAGGGTTATCTACCTCGGCGACGGCCGCGGCGACTACTGCCC
GTCGCTGCGCCTCGGTCGCGACGACTTCATGATGCCGCGCAAGGGCTTCCCCGTGTGGGAGCTCATCTGCGAGAACCCGT
CGCTGCTCCAGGCCGAGGTGCACCCGTGGACGGACGGCGCGGAGATGGAGGAGACGCTGCTGCGGCTGGTCGGCAGGGTG
CTCCTCGAGGCGAGGAACCTGCCGCCGCTCGACTGCAAGCTCGAGTCGTTGCCGGCCGTCGCCGTGCAGGACGGCATGCC
CATGCCGCTCCGGATCAAGAACTGA

Alignment

ORF - retro_opun_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.15 %
• Parental protein coverage: 51.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAVVVFDFDRTIIEWDSDDWVITKLGASDAFRRLHPTMRWNPLMDRMMAELHAQGRSADDIRDCLKSAP
          A..VVVFDFD.TII..DSD.WV...LGA...F.RL.PTM.WN.LMD.MM.ELHA.G...DD..D.L.SAP
Retrocopy AGIVVVFDFDKTIIDVDSDNWVVDGLGATEEFERLLPTMPWNTLMDTMMGELHARGKTLDDVADVLRSAP

Parental  LDAHILSAITTASALGCDLRVVSDANAFFIETVLEHHGVLGCFSEISTNPARVD-GDGRLRISPFHDPDS
          LD.....AI.....LGCDLR..SDAN.FFI.T.L.HHG..G.FSEI.TNP..VD...GRLRI.P.HD...
Retrocopy LDPRVVAAIKACYGLGCDLRILSDANRFFIDTILDHHGLTGYFSEINTNPSAVDAATGRLRIAPYHDFHA

Parental  SPHGCSL--CPENMCKG
          .PHGC.L..CP.NMCKG
Retrocopy APHGCGLGICPPNMCKG

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_7 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA001283	1 retrocopy	retro_oind_8,
Brachypodium distachyon	BRADI2G42720	1 retrocopy	retro_bdis_19,
Zea mays	GRMZM2G035134	1 retrocopy	retro_zmay_14,
Hordeum vulgare	MLOC_52823	1 retrocopy	retro_hvul_27,
Oryza brachyantha	OB01G31280	1 retrocopy	retro_obra_4,
Oryza glumaepatula	OGLUM01G25430	1 retrocopy	retro_oglu_22,
Oryza meridionalis	OMERI01G19970	1 retrocopy	retro_omer_22,
Oryza nivara	ONIVA01G24910	1 retrocopy	retro_oniv_37,
Oryza punctata	OPUNC01G21870	1 retrocopy	retro_opun_7 ,
Oryza rufipogon	ORUFI01G24440	1 retrocopy	retro_oruf_27,