RetrogeneDB ID: retro_oind_6

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 1:32188931..32189951(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA000960
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA028079
• Aliases: None
• Description: None

Sequence

>retro_oind_6
ATGGCTCGCGATTTTACGGCGACGTTTCTTCTGCTGCTCAGCGTCGCGTCGCTGCTGGTGATCTCGCCGTGCGCGGCCCA
GCAGATCAAGACCACCGACACGCGGTGGAGCTACCACCTCCCGCTTCCCGACGGCGTCAGCGGCGCCGAGAGCCTCGCCT
TCGACGGCAAGGACGGCCTCTACACCGGCGTCTCGGACGGCCGCGTGCTCAAGTGGGGAGGCAGCGCCGCCGGCTGGACC
ACGTTCGCGTACAATGCGAACTACCGGAAAATCCCTCTCTGCTCGTCGTCCGAGGTGCCACCGGAGGAGAGGGAGAGCAT
CTGCGGGCGCCCGCTGGGGATCCGGTTGTTCAGGAAGACCGGCGAGCTCTACATCGCCGACGCGTACAAGGGGCTGATGA
AGGTCGGGCCCGACGGCGGCGAGGCCCAGGTGGTCGCGACCGAGGCGGACGGCGTCCCCTTCCACTTCCTCAATGGCCTT
GACGTCGACCAAGCTACGGGTGATGCCTACTTCACCGACAGCAGCAGCACGTACACCCGCAGGTTCAACGGGGAGATCAC
GATGAACGCCGACGCGACAGGGCGGCTGCTCAAGTACGACGCGCGGACGCGGCGGGTCACCGTGCTGAAGACCGACCTGC
CGTACCCGAACGGCGTCGCCGTCAGCCGAGACAGGACGCACCTCGTCGTGGCGCACACCGTGCCGTGCCAGGCGTTCCGG
TACTGGCTGCGGGGCACCAAAGCCGGCGAGTACGAGCTCTTCGCCGACCTCCCGGGCTACCCCGACAACGTGAGGCGCGA
CACCAAGGGAGGCTACTGGGTGGCGCTCAACCAGGAGAGGATGCGGCTGGGCGCGGCGCCCGCAGCCAAGCACCTGGTCG
GCGTACGGCTCAACCCCGACGGCGTGGAGGTGGAGGAGTTGACGGCTACCAAGGGCGTCACGCTCAGCGAGGTGGCGGAG
CAGAAGGGCAAGCTGTGGTTGGGCTCCGTCGAACTCGATTACATTGGCATGTTTGCTTGA

Alignment

ORF - retro_oind_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 82.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGFPATLLVTLLRLVGCLLLVCLAAPPCAAQQVKTSHAQFAFHLPLPDGVTGAESLAFDSSNHGPYTGVS
          R.F.AT.L..LL..V..LL.......PCAAQQ.KT.......HLPLPDGV.GAESLAFD....G.YTGVS
Retrocopy RDFTATFL--LLLSVASLLVIS----PCAAQQIKTTDTRWSYHLPLPDGVSGAESLAFDGKD-GLYTGVS

Parental  HGRVLRWGGAAAGWTTFAHHQDYRKIPMCTTPVAPPEETESMCRRPLGLAFHDRTGDLYIADALH--MRV
          .GRVL.WGG.AAGWTTFA....YRKIP.C.....PPEE.ES.C.RPLG......TG.LYIADA....M.V
Retrocopy DGRVLKWGGSAAGWTTFAYNANYRKIPLCSSSEVPPEERESICGRPLGIRLFRKTGELYIADAYKGLMKV

Parental  GPRGGEAEVLAAGEDGVPFNFVNGIDVDQATGDVYFTDSSTTYPRRFNSEIMMNADATSRLLKYDAATKQ
          GP.GGEA.V.A...DGVPF.F.NG.DVDQATGD.YFTDSS.TY.RRFN.EI.MNADAT.RLLKYDA.T..
Retrocopy GPDGGEAQVVATEADGVPFHFLNGLDVDQATGDAYFTDSSSTYTRRFNGEITMNADATGRLLKYDARTRR

Parental  VTVLRSGLPYANGVAVSRDGSHAVVAHTVPCQAFRYWIKGPNAGEYELLADLPGYPDNVRRDARGGYWVA
          VTVL...LPY.NGVAVSRD..H.VVAHTVPCQAFRYW..G..AGEYEL.ADLPGYPDNVRRD..GGYWVA
Retrocopy VTVLKTDLPYPNGVAVSRDRTHLVVAHTVPCQAFRYWLRGTKAGEYELFADLPGYPDNVRRDTKGGYWVA

Parental  LNQEKVRLDATAAA
          LNQE..RL.A..AA
Retrocopy LNQERMRLGAAPAA

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_6 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA028079	1 retrocopy	retro_oind_6 ,
Oryza glumaepatula	OGLUM08G04830	1 retrocopy	retro_oglu_15,
Oryza meridionalis	OMERI08G04560	1 retrocopy	retro_omer_14,
Oryza punctata	OPUNC08G04420	1 retrocopy	retro_opun_39,
Oryza glaberrima	ORGLA08G0040000	1 retrocopy	retro_ogla_41,
Oryza rufipogon	ORUFI08G05030	1 retrocopy	retro_oruf_9,
Oryza sativa japonica	OS08G0175000	1 retrocopy	retro_osat_11,