RetrogeneDB ID: retro_oind_107

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: CH400582.1:506..1553(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA023742
• Aliases: None
• Description: None

Sequence

>retro_oind_107
GAATACTACAAAGGTATCGGCCAAATTAAATTTGAAGGAAAAGAATCAGACAATCCGCTGGCATTTAAATATTATAATCC
AGACCAAATTGTAGCTGGAAAAACAATGCGTGAGCACTTTAAATTTGCTATCGCATATTGGCATACATTCTGCGGACAAG
GAAGCGACCCATTTGGACCAGGAACACAGCAATTTGCTTGGGATCAGTCTTCAGATCCGTATCAGGCTGCAAAAGATAAA
GCAGATGCAGCTTTTGAATTTATCAGCAAAATGGGATTCGATTATTTCTGTTTCCATGATTATGATTTAATTGCTGAAGG
AGCAACTTTCGCAGAATCAGAAAAACGTTTGGCTTTTATTACAGATTACTTAAAACAGAAAAAAGCAGACTCTGGAATTA
AATTACTTTGGGGAACTTCAAACTGTTTCTCAAACCCAAGATTCATGAACGGAGCGGCTACAAATCCAGATTTTAATGTA
GTAGCAAGAGCCGGAGGACAAGTAAAATTAGCACTTGATGCAACAATTGCTTTAGGCGGAGAAAATTATGTATTCTGGGG
AGGTAGAGAAGGTTATATGTCTTTACTAAACACAGATATGGGAAGAGAATTAGACCACATGGCACAATTCCTTGCAATGT
CTAGAGACTACGCAAGAGCGCAAGGTTTTAAAGGAACTTTCTTTATCGAGCCAAAACCAATGGAACCATCAAAACACCAA
TACGATTTTGACTCGGCTACTGCAATTGGATTCTTGAAAAATTATGGTTTAGATAAAGATTTCAAAATCAATATCGAGGT
AAACCACGCTACTTTGGCGCAGCATACTTTCCAACACGAATTAGAAGTGGCTGCAAAAGCAGGAATGTTAGGAAGCATCG
ATGCAAACAGAGGAGATTACCAAAATGGCTGGGATACAGACCAGTTCCCAAATAACATTCAGGAAACGACTGAAGCAATG
TTGGTTTTCTTAAAAGCCGGGGGATTACAAGGCGGAGGAGTTAACTTTGATGCTAAAATTAGAAGAAATTCTACAGACTT
AGAAGAT

Alignment

ORF - retro_oind_107 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.3 %
• Parental protein coverage: 73.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EFFPGIPKIKYEGPSSKNPLAYKWYNAEEVILGKKMKDWMRFSVAFWHTFRGTGGDPFGAPTKSWPWEDG
          E...GI..IK.EG..S.NPLA.K.YN......GK.M.....F..A.WHTF.G.G.DPFG..T....W...
Retrocopy EYYKGIGQIKFEGKESDNPLAFKYYNPDQIVAGKTMREHFKFAIAYWHTFCGQGSDPFGPGTQQFAWDQS

Parental  TNSLDMAKRRMRAHFEFMEKLGVDRWCFHDRDIAPDGKTLTETNKNLDEIVELAKKLQEETNIKPLWGTA
          ......AK....A.FEF..K.G.D..CFHD.D....G.T..E..K.L..I....K.......IK.LWGT.
Retrocopy SDPYQAAKDKADAAFEFISKMGFDYFCFHDYDLIAEGATFAESEKRLAFITDYLKQKKADSGIKLLWGTS

Parental  QLFMHPRYMHGAATSPEVKVYAYGAAQVKKALEVTHYLGGENYVFWGGREGYQTLLNTDMKRELDHLASF
          ..F..PR.M.GAAT.P...V.A....QVK.AL..T..LGGENYVFWGGREGY..LLNTDM.RELDH.A.F
Retrocopy NCFSNPRFMNGAATNPDFNVVARAGGQVKLALDATIALGGENYVFWGGREGYMSLLNTDMGRELDHMAQF

Parental  LQAAVDYKKKIGFNGTLLIEPKPQEPTKHQYDWDVATTFSFLQKYGLTGEFKINVECNHATLSGHSCHHE
          L....DY....GF.GT..IEPKP.EP.KHQYD.D.AT...FL..YGL...FKIN.E.NHATL..H...HE
Retrocopy LAMSRDYARAQGFKGTFFIEPKPMEPSKHQYDFDSATAIGFLKNYGLDKDFKINIEVNHATLAQHTFQHE

Parental  LETARINGLLGNIDANTGDPQIGWDTDQFLTDISEATLVMSSVVKNGGLAPGGFNFDAKLRRESTDVED
          LE.A...G.LG.IDAN.GD.Q.GWDTDQF...I.E.T..M....K.GGL..GG.NFDAK.RR.STD.ED
Retrocopy LEVAAKAGMLGSIDANRGDYQNGWDTDQFPNNIQETTEAMLVFLKAGGLQGGGVNFDAKIRRNSTDLED

Legend:

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

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_107 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA023742	1 retrocopy	retro_oind_107 ,