RetrogeneDB ID: retro_oglu_47

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 8:4052143..4053622(+)
• Located in intron of: OGLUM08G04980

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM07G00430
• Aliases: None
• Description: None

Sequence

>retro_oglu_47
ATGGCGGGCGGCGCGATGGTCCAGACGGTGGGTGGCAAGACGTACCCGGGGAAGATGACCGCGTTCGTGTTCTTCACCTG
CCTCGTCGCCTCCTCCGGCGGCCTCATCTTCGGCTACGACATCGGCATCTCCGGCGGCGTCACCTCCATGGACTCCTTCC
TCAGCGAGTTCTTCCCGTCGGTGTACGCGCAGGCGAAGGCGAGCAAGGACACCAACCAGTACTGCAAGTTCGACAGCCAG
CTGCTGACCCTCTTCACCTCGTCGCTGTACCTGGCGGCGCTGGCGACGTCGTTCGTGGCGGCGTGGGTCACCCGGGTGTT
CGGCCGGAAGTGGTCCATGTTCTGCGGCGGCGTCACGTTCCTCGCCGGCTCGGCGCTCAACGGCGCCGCCACCGACGTCA
TGATGCTCATCCTCGGCCGCATCCTCCTCGGCGTCGGCGTCGGCTTCGCCAACCAGTCCGTGCCGCTCTACCTGTCGGAG
ATGGCGCCGGCGAACCTCCGCGGGATGCTCAACATCGGCTTCCAGCTCATGACCACCATCGGCATCCTCTCCGCCAACCT
CATCAACTACGCGACGTCGAGCATCGAGGGAGGGTGGGGGTGGCGCATCGGGCTCGGCCTCGCCGGCGTGCCCGCGCTCA
TCATCACGCTCGGCGCGCTCGTCCTCCCGGACACCCCAAACTCCCTCATCGCCCGCGGCTACGCCGGCGACGCCAAGCGC
GTCCTCGTCAAGATCCGCGGCACCGACGACGTCCACGACGAGTACGACGACATGGTAGCGGCAAGCGAAGAAGCCGCCTC
GATCGAACACCCATGGCGGAACATCCTCCAGCGCAAGTACCGCCCGCAGCTCACCATCGCCATCCTCATCCCGTGCTTCC
AACAACTCACCGGCATCAACGTGATCATGTTCTACGCGCCGGTGCTCTTCCTCACCATCGGCTTCGCCGGCGACGCGTCG
CTCATGTCCGCGGTGATCACGGGACTCGTCAACATGTTCGCCACCGTCGTCTCGATCATCTCCGTGGACCGCCTCGGCCG
CCGCGTGCTGTTCCTCCAGGGCGGCACGCAGATGTTCATCTCCCAGGTGGTGGTCGGGACGCTGATCGCGCTCCAGTTCG
GCGTCGCGGGCGTCGGCGAGATGTCGCGGTCGTACGCGATCTTGCTCGTGCTGTTCATCTGCATGTACGTGGCCGGGTTC
GCGTGGTCGTGGGGGCCCCTGGGGTGGCTGGTGCCGAGCGAGGTGTTCGCGCTGGAGATCAGGTCGGCGGGGCAGAGCAT
CGCGGTGTGCGTGAACATGATGCTGACGTTCGTCATCGGGCAGGCGTTCCTCACCATGCTGTGCCACCTCAAGTTCGGCC
TCTTCTACTTCTTCGCCGGGTGGATGCTGGTCATGACCACCTTCGTCGCGCTCTTCCTGCCGGAGACCAAGGGGGTGCCC
ATCGAGGAGATGAACCACGTCTGGAGCCGGCACTGGTTC

Alignment

ORF - retro_oglu_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 95.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGGAVVSTGAGKDYPGKLTLFVFFTCVVAATGGLIFGYDIGISGGVTSMDPFLRKFFPEVYRKKQMADK
          MAGGA.V.T..GK.YPGK.T.FVFFTC.VA..GGLIFGYDIGISGGVTSMD.FL..FFP.VY........
Retrocopy MAGGAMVQTVGGKTYPGKMTAFVFFTCLVASSGGLIFGYDIGISGGVTSMDSFLSEFFPSVYAQAKASKD

Parental  NNQYCKYDNQLLQTFTSSLYLAALVSSFFAATVTRVLGRKWSMFAGGLTFLIGAALNGAAENVAMLIVGR
          .NQYCK.D.QLL..FTSSLYLAAL..SF.AA.VTRV.GRKWSMF.GG.TFL.G.ALNGAA..V.MLI.GR
Retrocopy TNQYCKFDSQLLTLFTSSLYLAALATSFVAAWVTRVFGRKWSMFCGGVTFLAGSALNGAATDVMMLILGR

Parental  ILLGVGVGFANQSVPVYLSEMAPARLRGMLNIGFQLMITIGILAAELINYGTAKIKAGWGWRVSLALAAV
          ILLGVGVGFANQSVP.YLSEMAPA.LRGMLNIGFQLM.TIGIL.A.LINY.T..I..GWGWR..L.LA.V
Retrocopy ILLGVGVGFANQSVPLYLSEMAPANLRGMLNIGFQLMTTIGILSANLINYATSSIEGGWGWRIGLGLAGV

Parental  PAAIITLGSLFLPDTPNSLIDRGHPEAAERMLRRIRGSDVDVSEEYADLVAASEESKLVQHPWRNILRRK
          PA.IITLG.L.LPDTPNSLI.RG....A.R.L..IRG.D.DV..EY.D.VAASEE.....HPWRNIL.RK
Retrocopy PALIITLGALVLPDTPNSLIARGYAGDAKRVLVKIRGTD-DVHDEYDDMVAASEEAASIEHPWRNILQRK

Parental  YRAQLTMAICIPFFQQLTGINVIMFYAPVLFDTLGFKSDASLMSAVITGLVNVFATLVSIFTVDRLGRRK
          YR.QLT.AI.IP.FQQLTGINVIMFYAPVLF.T.GF..DASLMSAVITGLVN.FAT.VSI..VDRLGRR.
Retrocopy YRPQLTIAILIPCFQQLTGINVIMFYAPVLFLTIGFAGDASLMSAVITGLVNMFATVVSIISVDRLGRRV

Parental  LFLQGGAQMVVCQVVVGTLIAVKFGTSGIGDIPKGYAAVVVLFICMYVAGFAWSWGPLGWLVPSEIFPLE
          LFLQGG.QM...QVVVGTLIA..FG..G.G.....YA...VLFICMYVAGFAWSWGPLGWLVPSE.F.LE
Retrocopy LFLQGGTQMFISQVVVGTLIALQFGVAGVGEMSRSYAILLVLFICMYVAGFAWSWGPLGWLVPSEVFALE

Parental  IRPAGQSINVSVNMLFTFVIAQAFLTMLCHMKFGLFYFFAGWVVIMTVFIALFLPETKNVPIEEMVLVWK
          IR.AGQSI.V.VNM..TFVI.QAFLTMLCH.KFGLFYFFAGW...MT.F.ALFLPETK.VPIEEM..VW.
Retrocopy IRSAGQSIAVCVNMMLTFVIGQAFLTMLCHLKFGLFYFFAGWMLVMTTFVALFLPETKGVPIEEMNHVWS

Parental  SHWF
          .HWF
Retrocopy RHWF

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glumaepatula was not studied using ChIP-Seq data.

EST

Oryza glumaepatula was not studied using EST data.

TSS

Oryza glumaepatula was not studied using FANTOM5 data.

Lab

retro_oglu_47 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glumaepatula 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	BGIOSGA024972	1 retrocopy	retro_oind_19,
Medicago truncatula	MTR_0009s0370	1 retrocopy	retro_mtru_23,
Oryza barthii	OBART07G00410	1 retrocopy	retro_obar_21,
Oryza glumaepatula	OGLUM07G00430	1 retrocopy	retro_oglu_47 ,
Oryza glumaepatula	OGLUM07G18360	1 retrocopy	retro_oglu_7,
Oryza rufipogon	ORUFI07G00430	1 retrocopy	retro_oruf_37,
Oryza sativa japonica	OS07G0106200	1 retrocopy	retro_osat_43,