RetrogeneDB ID: retro_osat_36

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 1:89824..91411(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS01G0102000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS03G0826600
• Aliases: None
• Description: None

Sequence

>retro_osat_36
ATGGGTCGGCGGCTGTTGCTGCTCTTCCTAATGCTGGCACAGGCACCCAATTCCAATGGGGATTCCAAGATAAAGAACGT
GGTGGTGTTGGCGCTGGAGAACCGGTCGTTCGACCACATGCTGGGGTGGATGCAGCGGCTGCTGGGCCTCCCCATCGACG
GCCTCACCGGCGCAGAGTGCAACCCGGCTCCAGGACCAGGTCCAGCCGACTCCCTCCTCCACTGCGTCTCCCCCGACGCC
GACCTCGTCGTCCCCGACGACCCCGCCCACGCCTTCGAGGACGTCCTCGAGCAGCTGCTGGGGTTCCGACCCAATGACTC
TACTGGCGCCGCCGCCTCCCCCTCAGACATGTCGGGCTTCGTCCGCAGCGCCGTCTCCGTGAGCGCGCTCCTGACCGACG
CCGTCATGCGGGGGTTCACCCCGTCGCGGCTCCCGGCCTTCTCCGCGCTGGCCTCCTCCTTCGCGGTGTTCGACCGCTGG
TTCTCCTCCATCCCGGGGCCCACGCAGCCCAACCGGCTGTTCCTCTACTCCGCCACCTCCCACGGCGCCGTCGCCCACGA
CAAGTGGAACCTCCTCCGCGGCTACCCGCAGCGCACCATCTTTGACTCCCTCGCCGCCGACGCCCTCGACTACCGGGTCT
ACTTCAAGACCATCCCCACCACCCTCTTCTACCGCCGCCTCCGCACCGTCGCCAACGCCGCCCGCGGCACCTTCCGCCGC
TACGACGCCGCCTTCCGCGACCACGCCCGCAGGGGCCTCCTCCCGGCGCTCTCCGTCATCGAGCCACGCTACTTCGACCT
CACCGGCACGCCCGCCGACGACGACCACCCGGCGCACGACGTCGCCAACGGCCAGAGGCTGGTCAAGGACGTCTACGAGG
CGCTGCGGGCGGGCCCGCAGTGGAACCACACACTGCTCATCATCACCTACGACGAGCACGGCGGCTTCTACGACCACGTC
CCGCCGCCCAATGTCGGCGTCCCCAGCCCCGACGCCATCCGTGGCCCGCTGCCCTTCTTCTTCAGGTTCGACCGCCTCGG
CGTCAGGGTGCCCACCATCATGGTGTCGCCGTGGATCAGGAAAGGGACGGTGGTGGGGAGGCCGCCGGGAGGGCCAACGC
CCACGTCCGAGTACGAGCACTCCTCCATCCCGGCCACCATCAAGAAGATATTCAACCTCAGCTCCGACTTCCTCACCAGG
AGGGATGCGTGGGCGGGCACCTTCGAGCACCTCTTCACGGACCTGGACGAGCCAAGGACGGATTGCCCGGAGACATTGCC
GGAGATCCCGCCGCCATCTTCCTCGTCGTCGTCGACCAAGAAAGAAGACGGAGGATGGCTGTCGGACTTCCAGCGCGAGC
TGGTGCAGCTGGCGGCCTTCCTCAACGGCGACTACATGCTGTCAAGCTTCGCACAGGAGTACGAGTCGAGAATGACGATG
ACGGTGAAGCAGGCGGATGCGTATGTGAGGCGAGCCGTCAAAAGTTTCCTGGAGGCCAGCAAGCGGGCCAAACGCTTAGG
TGCAAACGACTCCGCCATTGTAACCATGAGACCATCCCTCACTACTGCAACCACCTGCTGCCCTTAG

Alignment

ORF - retro_osat_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.45 %
• Parental protein coverage: 79.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPIKTVVVVVMENRSFDHILGWLSRTRP-DIDGLNGTQSNRLNASDPSSPEIF-VTDEAGYV-DSDPGHG
          S.IK.VVV...ENRSFDH.LGW..R.....IDGL.G...N......P.......V...A..V...DP.H.
Retrocopy SKIKNVVVLALENRSFDHMLGWMQRLLGLPIDGLTGAECNPAPGPGPADSLLHCVSPDADLVVPDDPAHA

Parental  FEDIREQIFG---SADTSAVPAP--MSGFAQNARGMGLGMPQNVMSGFKPESVPVYAALADEFAVFDRWF
          FED..EQ..G......T.A...P..MSGF...A..........VM.GF.P...P...ALA..FAVFDRWF
Retrocopy FEDVLEQLLGFRPNDSTGAAASPSDMSGFVRSAVSVSALLTDAVMRGFTPSRLPAFSALASSFAVFDRWF

Parental  ASVPTSTQPNRLYVHSATSHGLTFNARKDLIHGFPQKTIFDSLEENGLSFGIYYQNIPATLFYQSLRRLK
          .S.P..TQPNRL...SATSHG........L..G.PQ.TIFDSL....L....Y...IP.TLFY..LR...
Retrocopy SSIPGPTQPNRLFLYSATSHGAVAHDKWNLLRGYPQRTIFDSLAADALDYRVYFKTIPTTLFYRRLRTVA

Parental  HLVK--FHQYSLKFKLHAKWGKLPNYAVIEQRYFDCEMFPANDDHPSHDVARGQRFVKEVYETLRASPQW
          ......F..Y...F..HA..G.LP...VIE.RYFD....PA.DDHP.HDVA.GQR.VK.VYE.LRA.PQW
Retrocopy NAARGTFRRYDAAFRDHARRGLLPALSVIEPRYFDLTGTPADDDHPAHDVANGQRLVKDVYEALRAGPQW

Parental  NETALIITYDEHGGFYDHVPTPVVGVPQPDGIVGPDPYYFKFDRLGVRVPSFLISPWIEKRTVI-HEPNG
          N.T.LIITYDEHGGFYDHVP.P.VGVP.PD.I.GP.P..F.FDRLGVRVP....SPWI.K.TV....P.G
Retrocopy NHTLLIITYDEHGGFYDHVPPPNVGVPSPDAIRGPLPFFFRFDRLGVRVPTIMVSPWIRKGTVVGRPPGG

Parental  PQDSSQYEHSSIPATVKKLFNLHSNFLTKRDAWAGTFENYFKIRKTPRTDCPEKLPEV--TKSLQPFGPK
          P...S.YEHSSIPAT.KK.FNL.S.FLT.RDAWAGTFE..F.....PRTDCPE.LPE.....S......K
Retrocopy PTPTSEYEHSSIPATIKKIFNLSSDFLTRRDAWAGTFEHLFTDLDEPRTDCPETLPEIPPPSSSSSSTKK

Parental  EDSS-LSEFQVELIQLASQLNGDHVLNTY
          ED...LS.FQ.EL.QLA..LNGD..L...
Retrocopy EDGGWLSDFQRELVQLAAFLNGDYMLSSF

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_36 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glumaepatula	OGLUM03G39370	1 retrocopy	retro_oglu_2,
Oryza sativa japonica	OS03G0826600	1 retrocopy	retro_osat_36 ,