RetrogeneDB ID: retro_osat_3

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 4:20954566..20955604(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS04G0423800
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS01G0543100
• Aliases: None
• Description: None

Sequence

>retro_osat_3
ATGGCGGCGACATTGCGTTGGGGCGGCGGCGGGCTCGCGGTGGCGGCGTTTGCGGCGGTGGTCGCGTTGTCCGGCCTCCT
CGGCGTCGCGGCGAACTACGGCGGCGGCGGCGGGTTCTTGTTCCCGCAGTTCTATCAGCACACGTGCCCGCAGATGGAGG
CGGTGGTGGGCGGCATCGTGGCGAGGGCGCACGCCGAGGACCCGCGCATGGCGGCGTCGCTGCTGCGGATGCACTTCCAC
GACTGCTTCGTGCAGGGGTGCGACGCGTCGGTGCTGCTCGACGCCGACGGCAGCGGGCGGTTCGCCACGGAGAAGCGGTC
CAACCCCAACCGCGACTCGCTGCGCGGGTACGAGGTGATCGACGAGATCAAGGCCGCCCTGGAGCACGCGTGCCCGCGCA
CCGTCTCCTGCGCCGACATCGTCGCCGTCGCCGCCAGGGACTCCACCGCGCTCACCGGCGGGCCGTGGTGGGAGGTGCCC
CTCGGCAGGCGGGACTCGCTGACGGCCAGCCTGAGCGGCTCCAACAACCTCATCCCGGCGCCCAACGACACGCTCCCCAC
CATCGTCGGCAAGTTCCGCAACCAGGGCCTCGACGTCGTCGACCTCGTCGCGCTCTCCGGCGGCCACACCATCGGCAACT
CCCGGTGCGTCAGCTTCCGCCAGAGGCTGTACGGCCAGCTGAACAGCGACGGGAAGCCGGACTTCACCCTGAACCCGGCG
TACGCGGCGGAGCTCCGGGAGCGGTGCCCGAGCTCCGGCGGCGACCAGAACCTGTTCGCGCTGGACCCGGCCAGCCAGTT
CCGGTTCGACAATCAGTACTACCGCAACATCCTCGCCATGAACGGCCTCCTCAGCTCCGACGAGGTGCTCCTCACCAAGA
GCCGGGAGACGATGGAGCTCGTCCACCGCTACGCCGCCAGCAACGAGCTCTTCTTCGCGCAGTTCGCCAAGTCCATGGTC
AAGATGGGCAGCATCTCCCCGCTCACCGGCCACAACGGCGAGATCAGGATGAACTGCAGGAGGGTCAACCACTTCTAG

Alignment

ORF - retro_osat_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.24 %
• Parental protein coverage: 89.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDPHFYDHSCPQAQQIVASIVGKAHYQDPRMAASLLRLHFHDCFVKGCDASILLDS--SATIMSEKRSNP
          L.P.FY.H.CPQ....V..IV..AH..DPRMAASLLR.HFHDCFV.GCDAS.LLD...S.....EKRSNP
Retrocopy LFPQFYQHTCPQMEAVVGGIVARAHAEDPRMAASLLRMHFHDCFVQGCDASVLLDADGSGRFATEKRSNP

Parental  NRDSARGFEVIDEIKAALEAACPHTVSCADILALAARDSTVMTGGPGWIVPLGRRDSRGASVQGSNNDIP
          NRDS.RG.EVIDEIKAALE.ACP.TVSCADI.A.AARDST..TGGP.W.VPLGRRDS..AS..GSNN.IP
Retrocopy NRDSLRGYEVIDEIKAALEHACPRTVSCADIVAVAARDSTALTGGPWWEVPLGRRDSLTASLSGSNNLIP

Parental  APNNTLPTIITKFKLQGLDIVDLVALLGSHTIGDSRCTSFRQRLYNQ-TGNGLPDFTLDASYAAALRPRC
          APN.TLPTI..KF..QGLD.VDLVAL.G.HTIG.SRC.SFRQRLY.Q....G.PDFTL...YAA.LR.RC
Retrocopy APNDTLPTIVGKFRNQGLDVVDLVALSGGHTIGNSRCVSFRQRLYGQLNSDGKPDFTLNPAYAAELRERC

Parental  PRSGGDQNLFFLDPVTPFRFDNQYYKNLLAHRGLLSSDEVLLTGGNPATAELVELYAADQDIFFAHFARS
          P.SGGDQNLF.LDP...FRFDNQYY.N.LA..GLLSSDEVLLT.....T.ELV..YAA....FFA.FA.S
Retrocopy PSSGGDQNLFALDPASQFRFDNQYYRNILAMNGLLSSDEVLLTKSR-ETMELVHRYAASNELFFAQFAKS

Parental  MVKMGNISPLTGGNGEVRTNCRRVNH
          MVKMG.ISPLTG.NGE.R.NCRRVNH
Retrocopy MVKMGSISPLTGHNGEIRMNCRRVNH

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_3 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA003712	1 retrocopy	retro_oind_39,
Oryza brachyantha	OB01G28610	1 retrocopy	retro_obra_12,
Oryza sativa japonica	OS01G0205900	1 retrocopy	retro_osat_17,
Oryza sativa japonica	OS01G0543100	1 retrocopy	retro_osat_3 ,