RetrogeneDB ID: retro_oind_16

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 5:29080005..29081871(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA017582
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA004194
• Aliases: None
• Description: None

Sequence

>retro_oind_16
ATGGGGTCGTCGTCCCTCCCCCGCGCGGCCGTCCTCGCCGTGGCGCTCCTCCTCCTCGCCGACTCCGGCGAGGCGTTCTT
CGACCTCTTCAGCATCTTCCGCCCGCGCTCCGACAGCGATTACTTCCCGTTCGATGGGTCGGCGGGGCAGGCGAAGCGGA
AGCCGAAGATCGAGCAGGAGGAGGATGGCGCCGCGCCGGCCACAGCCACGGGCCTCACCAAGGTGCCGCCGCTGGGCGCG
CCCAGCAAGGCGGCGCTCGACACCATCGTCCTCCCCGTCGACGACTCCGCGGGGCACGCCGGGTCGTGGACCATCGTCAG
CGAGAACTCCGGCGTGTCGGCGATGCACCTCGCCGTCATGCGCCACGGCAAGGCCATCATGTTCGACACCAGCACCACCG
GCCGGTCGCTGATGCGCCTCCCCATGAATAACTGCCGCGCCGACCCGCGCGCCAAGAGGGAAGGCACCATGGACTGCTGG
GCGCACGCCGTGGAGTTCGACTACAGCACCGGCGCGCTCCGGTCGCTCAAGACCGCCACCGACACGTGGTGTTCGTCCGG
CGCGTTCGACGCCGACGGCAACCTGATCCAGACCGGTGGCTACTTCGAGGGCGACAAGGCGGTGAGGCGGCTCGACGCGT
GCGACACCTGCGACTGGCGCGAGTACCCGAACAGCTTCGCCGAGGGGAGGTGGTACGCGACGCAGCAGGTGCTCCCCGAC
GGGCGGTTCATCGTGTTCGGCGGCCGGCGAGCCTTCAGCTACGAGTTCGTGCCGCAGCCGGGGATGACCAACGGCCAGTC
CATCAAGTTCCCGCTCCTCCGCGAGACCACCGACGACGTCGAGAACAACCTCTACCCGTTCGTCAACCTCCTCCCCGACG
GCAACCTCTTCGTCTTCGCCAACGACCGCTCCGTCGTCTTCGACCACAGGACGGGCAAGGTCGTCCGCGAGCTCCCCAAG
CTCGCCGGCGGCGGGCGGAACCACCCGGCGTCGGCCATGTCGGCGATGCTCCCGCTCGACCTCCGCAACCTGACCCGCGG
CGCCGACCCGGAGCCGGAGGTGATCGTCTGCGGCGGCGCGCTCAAGACGGCGTTCAGGCTGGGGGAGAACAACACGTACC
AGCCGACGCTCCGCGACTGCGCCCGCATCAACCTGGGCAAGATCGACGCGGTGTGGGCGGTGGAGGCGATGCCGGTGGGC
CGCGTCATGGGCGACCTGCTCGTCCTCCCCACCGGCGACCTGCTCATGCTCAACGGCGCCGCCAAGGGGAGCTCCGGGTG
GGGGTTCGCGCGGCAGCCCATCCTGTCGCCGATCCTCTACTCGCCGCGGCACCCGGAGGGGTCGCGGTTCCGGCCGCTGG
CGGCGTCGACGGTGGCGCGGATGTACCACTCCACCAGCGCCGTGCTCCCGGACGCCACGGTGCTGGTCGCCGGCGGGAAC
ACGAACGCGGCGTACAACTTCAGCGGCGTGGACTTCCCGACGGAGGTGCGGGTGGAGCGGTTCGCGCCGCCGTACCTGAG
CAGGGAGCTGACCGGGAACCGGGCGGTGATCGACGTGGCGTCGGTGCCGGCGGGCGGGATGCGGTACGGGACCAAGTTCA
CGTTCAGGTTCCACACGCCGGTGGCGGCGGTGGAGTGGGGCGACGTGAGGGTGACCATGTACGCGCCGCCCTTCACGACG
CACGGCTACTCCATGAACCAGCGCTTGCTCGTGCTGCCCGTCGCCGGCTTCTCGGCGCAGGGGCAGATGTACGAGCTCAC
CGTCGACACGCCGCGGAAGCCGGAGCTCGCGCCGCCGGGGTACTACCTCGTCTACGTCGTATCCAAGGACGTGCCCAGCG
AGGCCGCTTGGGTCAAAATACAGTAA

Alignment

ORF - retro_oind_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.29 %
• Parental protein coverage: 89.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQQELGAAGPGGSGLSKAPPRSAPSKVALDSLKLPVDTSAGFAGGWNLVSENSGVSAMHLVVMQHGKAIM
          EQ.E.GAA.....GL.K.PP..APSK.ALD...LPVD.SAG.AG.W..VSENSGVSAMHL.VM.HGKAIM
Retrocopy EQEEDGAAPATATGLTKVPPLGAPSKAALDTIVLPVDDSAGHAGSWTIVSENSGVSAMHLAVMRHGKAIM

Parental  FDTCTTGRSLMRLPPGRCRPDPRSKQPGAMDCWAHAVEFDYNTGALRSLKIVTDTWCSSGAFDADGNMVQ
          FDT.TTGRSLMRLP...CR.DPR.K..G.MDCWAHAVEFDY.TGALRSLK..TDTWCSSGAFDADGN..Q
Retrocopy FDTSTTGRSLMRLPMNNCRADPRAKREGTMDCWAHAVEFDYSTGALRSLKTATDTWCSSGAFDADGNLIQ

Parental  TGGFFEGDKSVRYLSACGTCDWKEFPKSLADGRWYGTQLVLPDGSFIVIGGRRAFSYEFVPAAGRANARA
          TGG.FEGDK.VR.L.AC.TCDW.E.P.S.A.GRWY.TQ.VLPDG.FIV.GGRRAFSYEFVP..G..N...
Retrocopy TGGYFEGDKAVRRLDACDTCDWREYPNSFAEGRWYATQQVLPDGRFIVFGGRRAFSYEFVPQPGMTNGQS

Parental  TPLRLLRDTTDDVENNLYPFVNLLPDGTLFIFANDRSIVFNYRTGQVVRELPILPGGARNYPASAMSTLL
          ....LLR.TTDDVENNLYPFVNLLPDG.LF.FANDRS.VF..RTG.VVRELP.L.GG.RN.PASAMS..L
Retrocopy IKFPLLRETTDDVENNLYPFVNLLPDGNLFVFANDRSVVFDHRTGKVVRELPKLAGGGRNHPASAMSAML

Parental  PLDLR---KGAGLSAEVIICGGATKNAFKLGETGTFPPALRDCARINPSKPGARWALDQMPSGRVMGDVL
          PLDLR....GA....EVI.CGGA.K.AF.LGE..T..P.LRDCARIN..K..A.WA...MP.GRVMGD.L
Retrocopy PLDLRNLTRGADPEPEVIVCGGALKTAFRLGENNTYQPTLRDCARINLGKIDAVWAVEAMPVGRVMGDLL

Parental  ILPTGDLLMLNGAAKGCSGWGFGRQALLSPVLYSPYLRRGKRFRVLNPSNIPRMYHSTSALLPDATVLVA
          .LPTGDLLMLNGAAKG.SGWGF.RQ..LSP.LYSP....G.RFR.L..S...RMYHSTSA.LPDATVLVA
Retrocopy VLPTGDLLMLNGAAKGSSGWGFARQPILSPILYSPRHPEGSRFRPLAASTVARMYHSTSAVLPDATVLVA

Parental  GSNTNSAYNFSGVDFPTEVRVERFTPPYLGPQLSPNRPAIDAASVPRDGMRYGARFTFRFTTPAQGVGQG
          G.NTN.AYNFSGVDFPTEVRVERF.PPYL...L..NR..ID.ASVP..GMRYG..FTFRF.TP...V..G
Retrocopy GGNTNAAYNFSGVDFPTEVRVERFAPPYLSRELTGNRAVIDVASVPAGGMRYGTKFTFRFHTPVAAVEWG

Parental  DVKVTMYAPPFTTHGYSMNQRLLILPVTAFAAQGQRHTVTVDAPPKPELAPPGYYMVYVVAKGVPSKAAW
          DV.VTMYAPPFTTHGYSMNQRLL.LPV..F.AQGQ....TVD.P.KPELAPPGYY.VYVV.K.VPS.AAW
Retrocopy DVRVTMYAPPFTTHGYSMNQRLLVLPVAGFSAQGQMYELTVDTPRKPELAPPGYYLVYVVSKDVPSEAAW

Parental  VKM
          VK.
Retrocopy VKI

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_16 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	BGIOSGA004194	1 retrocopy	retro_oind_16 ,
Brachypodium distachyon	BRADI2G46477	1 retrocopy	retro_bdis_13,
Oryza glumaepatula	OGLUM01G30230	1 retrocopy	retro_oglu_1,
Oryza meridionalis	OMERI01G24080	1 retrocopy	retro_omer_13,
Oryza glaberrima	ORGLA01G0215900	1 retrocopy	retro_ogla_7,
Oryza sativa japonica	OS01G0677000	1 retrocopy	retro_osat_22,
Setaria italica	Si004698m.g	1 retrocopy	retro_sita_36,