RetrogeneDB ID: retro_opun_36

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 8:4063061..4064612(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC08G04580
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC07G17520
• Aliases: None
• Description: None

Sequence

>retro_opun_36
ATGGCGGGCGGCGCGATGGTTCAGACGGTGGGGGGCAAGACGTACCCTGGGAAGATGACGGCGTTCGTGTTCTTCACCTG
CCTCGTGGCGTCCTCCGGCGGCCTCATCTTCGGCTACGACATCGGCATCTCCGGCGGCGTGACCTCCATGGATTCTTTCC
TCAGCGAGTTCTTCCCGTCGGTGTACGCCCAGGCGAAGGCGAACAAGGACACGAACCAGTACTGCAAGTTCGACAGCCAG
CTGCTGACGCTCTTCACGTCGTCGCTGTACCTGGCGGCGCTGGCGACGTCGTTCGTGGCGGCGTGGGTGACCCGGGTGTT
CGGCCGGAAGTGGTCCATGTTCTGCGGCGGCGTCACGTTCCTCGCCGGCTCGGCGCTCAACGGCGGCGCCACCGACGTGA
TGATGCTCATCCTGGGGCGCATCCTGCTCGGCGTCGGCGTCGGGTTCGCCAACCAATCCGTGCCGCTGTACCTGTCGGAG
ATGGCGCCGGCGAACCTCCGCGGGATGCTCAACATCGGGTTCCAGCTCATGACCACCATTGGCATCCTCTCCGCCAACCT
CATCAACTACGCGACGTCGAGCATCCAGGGAGGGTGGGGGTGGCGCATCGGCCTGGGGCTCGCCGGCGTGCCGGCGCTCA
TCATCACGCTCGGCGCGCTCGTCCTCCCGGACACCCCAAACTCCCTCATAGCCCGTGGCTACGCCGGCGACGCCAAGCGA
GTACTCGTCAAGATCCGCGGCACCGACGACGTCCACGACGAGTACGACGACATGGTCGCCGCGAGCGAGGAAGCCGCGGC
GATCGAGCACCCATGGCGGAACATCCTACAACGCAAATACCGCCCGCAACTAACGATCGCCATCCTCATACCATGCTTCC
AGCAACTCACCGGCATCAACGTGATCATGTTCTACGCCCCCGTCCTCTTCCTCACCATCGGCTTCGCCGGCGACGCGTCG
CTCATGTCCGCCGTCATCACCGGCCTCGTCAACATGTTCGCCACCGTCGTCTCCATCATCTCCGTCGACCGCCTCGGCCG
CCGCGCCCTGTTCCTCCAGGGCGGGACACAGATGTTCATCTCGCAGGTGGTGGTCGGCACCCTCATCGCGCTCCAGTTTG
GCGTCGCCGGCGTCGGCGAGATGTCGCGGTCGTACGCGATCCTCCTCGTCCTCTTCATCTGCCTCTACGTGGCCGGGTTC
GCGTGGTCGTGGGGGCCATTGGGGTGGCTGGTGCCGAGCGAGGTGTTCTCGCTGGAGATCAGGTCGGCGGGGCAGAGCAT
CGCGGTGTGCGTCAACATGATGCTCACCTTCATCATCGGCCAGGCGTTCCTCACCATGCTCTGCCACCTCAAGTTCGGCC
TCTTCTACTTCTTCGCCGCCTGGATGCTGGTCATGACCACCTTCGTCGCGCTCTTCTTGCCGGAGACCAAGGGGGTGCCC
ATCGAGGAGATGAACCACGTCTGGAGCCGCCACTGGTTCTGGGGAACCTACGTCTCGCCGCACGACGTCGCCGGCGCCGG
CGCCGGAAACCGCAGAAGCCACAACGTCTAA

Alignment

ORF - retro_opun_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.48 %
• Parental protein coverage: 95.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGGVVVNNGGGKDYPGKLTMFVLFACIVAATGGLIFGYDIGISGGVTSMNPFLIKFFPSVYRKEQAAEK
          MAGG..V...GGK.YPGK.T.FV.F.C.VA..GGLIFGYDIGISGGVTSM..FL..FFPSVY...QA...
Retrocopy MAGGAMVQTVGGKTYPGKMTAFVFFTCLVASSGGLIFGYDIGISGGVTSMDSFLSEFFPSVYA--QAKAN

Parental  NQSNQYCKFDSPLLTMFTSSLYLAALVASFFASTVTRVAGRKWSMFGGGVTFLVGAALNGAAKNVLMLIL
          ...NQYCKFDS.LLT.FTSSLYLAAL..SF.A..VTRV.GRKWSMF.GGVTFL.G.ALNG.A..V.MLIL
Retrocopy KDTNQYCKFDSQLLTLFTSSLYLAALATSFVAAWVTRVFGRKWSMFCGGVTFLAGSALNGGATDVMMLIL

Parental  GRVLLGIGVGFANQSVPLYLSEMAPARLRGMLNIGFQLMITIGILCANLINYGTAKIKGGWGWRVSLALA
          GR.LLG.GVGFANQSVPLYLSEMAPA.LRGMLNIGFQLM.TIGIL.ANLINY.T..I.GGWGWR..L.LA
Retrocopy GRILLGVGVGFANQSVPLYLSEMAPANLRGMLNIGFQLMTTIGILSANLINYATSSIQGGWGWRIGLGLA

Parental  AVPAAIIAVGALFLPDTPNSLIDRGHTDAAKRMLRRVRGTDDIEEEYNDLVAASEESKLVAHPWRNILQR
          .VPA.II..GAL.LPDTPNSLI.RG....AKR.L...RGTDD...EY.D.VAASEE.....HPWRNILQR
Retrocopy GVPALIITLGALVLPDTPNSLIARGYAGDAKRVLVKIRGTDDVHDEYDDMVAASEEAAAIEHPWRNILQR

Parental  RYRPQLTMAIAIPLFQQLTGINVIMFYAPVLFKTLGFADDASLMSAVITGLVNVFATFVSIVTVDRLGRR
          .YRPQLT.AI.IP.FQQLTGINVIMFYAPVLF.T.GFA.DASLMSAVITGLVN.FAT.VSI..VDRLGRR
Retrocopy KYRPQLTIAILIPCFQQLTGINVIMFYAPVLFLTIGFAGDASLMSAVITGLVNMFATVVSIISVDRLGRR

Parental  KLFLQGGTQMLACQIVVGSLIGAKFGFSGVADIPKAYAAFVVLFICAYVAGFAWSWGPLGWLVPSEIFPL
          .LFLQGGTQM...Q.VVG.LI...FG..GV......YA...VLFIC.YVAGFAWSWGPLGWLVPSE.F.L
Retrocopy ALFLQGGTQMFISQVVVGTLIALQFGVAGVGEMSRSYAILLVLFICLYVAGFAWSWGPLGWLVPSEVFSL

Parental  EIRSAGQSINVSVNMLFTFIIAQAFLPMLCRFKFILFFFFGAWVVIMTLFVAFFLPETKNVPIEEMVLVW
          EIRSAGQSI.V.VNM..TFII.QAFL.MLC..KF.LF.FF.AW...MT.FVA.FLPETK.VPIEEM..VW
Retrocopy EIRSAGQSIAVCVNMMLTFIIGQAFLTMLCHLKFGLFYFFAAWMLVMTTFVALFLPETKGVPIEEMNHVW

Parental  KSHWYWGRFIRDEDV
          ..HW.WG......DV
Retrocopy SRHWFWGTYVSPHDV

Legend:

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

Expression

RNA-Seq

Oryza punctata was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_36 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G24820	1 retrocopy	retro_bdis_38,
Hordeum vulgare	MLOC_55525	1 retrocopy	retro_hvul_80,
Medicago truncatula	MTR_0009s0370	1 retrocopy	retro_mtru_23,
Oryza glumaepatula	OGLUM07G18360	1 retrocopy	retro_oglu_7,
Oryza meridionalis	OMERI07G15470	2 retrocopies	retro_omer_15, retro_omer_8,
Oryza nivara	ONIVA07G16940	1 retrocopy	retro_oniv_2,
Oryza punctata	OPUNC07G17520	1 retrocopy	retro_opun_36 ,
Oryza glaberrima	ORGLA07G0149800	1 retrocopy	retro_ogla_30,
Oryza rufipogon	ORUFI07G19310	1 retrocopy	retro_oruf_45,
Oryza sativa japonica	OS07G0559700	1 retrocopy	retro_osat_29,
Triticum aestivum	Traes_2BS_7DF366FE1	1 retrocopy	retro_taes_36,