RetrogeneDB ID: retro_osat_46

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 1:25187249..25189517(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS01G0630200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS02G0695800
• Aliases: None
• Description: None

Sequence

>retro_osat_46
ATGGGCGAGGGCGAGTTCGTCGACGTCGAGCGCGGCGTGGTCGCTGAAGGGGCGTTGGACGACGACGCGTCGCCGATCGA
GGAGGTCCGGCTGACGGTTCCGGTCACTGACGACTCGTCCCTTCCGGTGTGGACGTTCCGGATGTGGACACTCGGCCTGC
TCTCGTGCGTGCTCATGAGCTTCCTGAACCAGTTCTTCTCCTACCGCACCGAGCCGCTCATCGTCACCCAGATCACCGTG
CAGGTGGCCTCGCTGCCTCTGGGCCACATCCTCGCCCGCGTGCTGCCGCGCCGCAAGTTCAAGGCCCCCGCGCTGCTCGG
CGGCGGGGAGTGCAGCCTCAACCCGGGGCCCTTCAACATGAAGGAGCACGTGCTCGTCTCCATCTTCGCCAACGCCGGCT
GCGCCTTCGGCAGCGGGTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACGGGCGGTCCATCTCCCTC
TTCCCCGCATGGCTCCTCATCACCACCACGCAGGTGCTCGGCTACGGGTGGGCGGGGCTGATGCGCAGGTACGTGGTGGA
GCCGGCGCAAATGTGGTGGCCCGGCACGCTCGTGCAGGTGTCGCTGTTCAGGGCGCTGCACGGGAAGGGGGAAGAGAAGG
AGGAGAATAAGGAGGGCAGCGGCGGCGGGATGTCTCAGGCCAAGTTCTTCCTGATCGCGCTCGCCTGCAGCTTCCTGTGG
TACGCCGTGCCGGGTTACCTGTTCCCGACGCTGACCTCCGTCTCGTGGGTCTGCTGGATCTTCTCCAAGTCCGTCACGGC
GCAGCAGCTGGGCTCCGGCATGAAGGGCCTGGGCCTCGGCGCCTTCACCCTCGACTGGACGGCCGTGTCAGCCTTCCTGT
ACAGCCCGCTGATCTCGCCGTTCTTTGCCACCGCCAACATCTTGGCCGGCTACGTGCTCCTGATGTACGTGGTCGTGCCG
GTGTCGTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTGTTCACGGCCACCGGCAG
CACATACGACATCACGGCCATCGTGAACGACCGCTTCGAGATCGACATGGACGGGTACCATCGGATGGGGCGGATCAACA
TGAGCACGTTCTTTGCGCTGTCCTACGGGCTCGGCTTCGCGACGATCGCGGCCACCGTCACGCACGTGGCGCTGTTCCAC
GGGAAGGAGATCTACCGCCGGTTCCGCGCGTCGCAGAGGGACAAGCCCGACGTGCACACGAGGCTGATGAAGAGCTACCG
CGACGTGCCGAGCTGGTGGTTCTACGCGATGCTCGCGCTGTCCATGGCCGTCTCGCTCTTGCTCTGCACCGTCCTCAGGT
CGGCGGTGCAGCTCCCGTGGTGGGGTCTCCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTGCCGATCAGCATCATC
ACGGCCACGACCAACCAGACGCCAGGGCTCAACATCATCACCGAGTACGTCATCGGGCTCATGCTTCCGGGCAAGCCCAT
CGCCAACGTCTGCTTCAAGGCGTACGGCTACATGAGCATGTCGCAGGCCGTGTCCTTCCTGTCCGACTTCAAGCTCGGCC
ACTACATGAAGATACCCCCCAAGTCCATGTTCCTCGTGAAGTTGGTCGGCACGGTGGTCGCCTCCACGGTCAACCTCGTG
GTGGCGTACTGGCTGCTGGGTTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCGGCGGATAGCCCGTGGACGTGCCC
GAACGACCGCGTCTTCTTCGACGCGTCCGTCATCTGGGGCCTCGTCGGGCCGCGCCGCATCTTCGGGCCACTCGGCAACT
ACGGCGCGCTCAATTGGTTCTTCCTCGCTGGCGCCGTGGGACCCGTCATTGTGTACTTGCTCCACAGGGCGTTCCCCAGC
AAGACCTGGATACCGATGATCAACCTGCCGGTGCTCATCGGAGCGACCTCCTACATGCCGCCGGCAACGGCCGTGAACTA
CAACTCCTGGCTGATCATCGGGATCATCTTCAACTTCTTCGTTTTCCGGTACAGGAAGCTGTGGTGGAAGAGGTACAACT
ACATCCTCTCGGCTGCGCTCGACGCCGGCGTCGCGTTCATGGCGGTGCTGCTCTACTTCTCGCTGTCGATGGAGAACCGG
AGCATCAGCTGGTGGGGTACGGCCGGCGAGCACTGCCCGCTGGCCTCATGCCCTACCGCCAAAGGGATAAACTTGGGCGC
TGATAGCGTCTGCCCTGTTGTGTTATAA

Alignment

ORF - retro_osat_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.13 %
• Parental protein coverage: 99.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTSISWVCWVFSKSVTAQQLGSGLKGLGVGAFSLDWTAISSFLFSPLISPFFATANIFVGFVLFLYVLVP
          LTS.SWVCW.FSKSVTAQQLGSG.KGLG.GAF.LDWTA.S.FL.SPLISPFFATANI..G.VL..YV.VP
Retrocopy LTSVSWVCWIFSKSVTAQQLGSGMKGLGLGAFTLDWTAVSAFLYSPLISPFFATANILAGYVLLMYVVVP

Parental  IAYWGFDLYNAKTFPIFSSHLFMSNGTSYDITAIVNDKFELDIDAYNKLGRINLSVFFALAYGLSFATIA
          ..YWG.DLYNA..FPIFSSHLF...G..YDITAIVND.FE.D.D.Y...GRIN.S.FFAL.YGL.FATIA
Retrocopy VSYWGLDLYNARRFPIFSSHLFTATGSTYDITAIVNDRFEIDMDGYHRMGRINMSTFFALSYGLGFATIA

Parental  STVTHVGLFYGKEIYHRFRASQKEKPDIHTRLMKKYDDIPVWWFYSLMALSMTVALILCTVLKHEVQLPW
          .TVTHV.LF.GKEIY.RFRASQ..KPD.HTRLMK.Y.D.P.WWFY...ALSM.V.L.LCTVL...VQLPW
Retrocopy ATVTHVALFHGKEIYRRFRASQRDKPDVHTRLMKSYRDVPSWWFYAMLALSMAVSLLLCTVLRSAVQLPW

Parental  WGLLFACGMAFIFTLPISIISATTNQTPGLNVITEYAIGLIIPGHPIANVCFKVYGYMSMSQAIAFLSDF
          WGLLFAC.MAF.FTLPISII.ATTNQTPGLN.ITEY.IGL..PG.PIANVCFK.YGYMSMSQA..FLSDF
Retrocopy WGLLFACAMAFVFTLPISIITATTNQTPGLNIITEYVIGLMLPGKPIANVCFKAYGYMSMSQAVSFLSDF

Parental  KLGHYMKIPPKSMFLVQFIGTIVAGTVNLGVAWWLLGSIHDICQDS-LPADSPWTCPNDRVFFDASVIWG
          KLGHYMKIPPKSMFLV...GT.VA.TVNL.VA.WLLGSI..ICQD..LPADSPWTCPNDRVFFDASVIWG
Retrocopy KLGHYMKIPPKSMFLVKLVGTVVASTVNLVVAYWLLGSIPNICQDALLPADSPWTCPNDRVFFDASVIWG

Parental  LIGPIRIFGPHGNYSALNWFFLIGAAGPVIVYIFHKMFPNKKWITLTNLPVLIGATASMPPATAVNYNSW
          L.GP.RIFGP.GNY.ALNWFFL.GA.GPVIVY..H..FP.K.WI...NLPVLIGAT..MPPATAVNYNSW
Retrocopy LVGPRRIFGPLGNYGALNWFFLAGAVGPVIVYLLHRAFPSKTWIPMINLPVLIGATSYMPPATAVNYNSW

Parental  LLFGTIFNFFVFRYRKKWWERYNYILSAALDAGVAFMAVLLYFSLSMENRSIDWWGTAGEHCPLATCPTA
          L..G.IFNFFVFRYRK.WW.RYNYILSAALDAGVAFMAVLLYFSLSMENRSI.WWGTAGEHCPLA.CPTA
Retrocopy LIIGIIFNFFVFRYRKLWWKRYNYILSAALDAGVAFMAVLLYFSLSMENRSISWWGTAGEHCPLASCPTA

Parental  KGVDLGPTSVCPV
          KG..LG..SVCPV
Retrocopy KGINLGADSVCPV

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_46 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	BGIOSGA005797	1 retrocopy	retro_oind_42,
Oryza nivara	ONIVA02G31600	1 retrocopy	retro_oniv_17,
Oryza sativa japonica	OS02G0695800	1 retrocopy	retro_osat_46 ,
Setaria italica	Si016420m.g	1 retrocopy	retro_sita_13,