RetrogeneDB ID: retro_oglu_7

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 9:7523903..7525481(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM09G05150
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM07G18360
• Aliases: None
• Description: None

Sequence

>retro_oglu_7
ATGCCGGGCGGCGGCGCGATGGTGGCGGCGGGCGGCGGCGGCGGCCGGCCGGAGTACCCGGGCGGGCTCACCATGTTCGT
CTCCATGGCGTGCCTCGTGGCGGCCACCGGCGGCCTCATCTTCGGCTACGACATCGGCGTCTCCGGCGGCGTCACCTCCA
TGGACCCGTTCCTCAGCAGGTTCTTCCCGTCGGTGTACCGCGCGCAGTCGGCAGCGGCGGCGGCGGCCGGCGGCGGAGGC
GGGAACCAGTACTGCAGGTTCGACAGCCCGCTGCTCACCATGTTCACCTCGTCGCTCTACCTCGCCGCGCTCGCCTCGTC
GCTCGGCGCCGCCACGGTGACGCGCGTGGCGGGGCGCAAGTGGTCCATGTTCGCCGGCGGGCTCGTGTTCCTCGCCGGGT
GCGCGCTCAACGGCGCGGCGGCGAACGTGGCGATGCTCATCGTCGGCCGCGTCCTGCTCGGCGTCGGCATCGGGTTCGCC
AACCAGAGCGTGCCGGTGTACCTGTCGGAGATGGCGCCGGCGAGGATGCGCGGGATGCTCAACAACGGCTTCCAGATGAT
GATCACCACCGGCGTGCTCGCCGCCAACCTCATCAACTACGGCACCGCCAGGATCGCCGGCGGGTGGGGGTGGCGCCTCA
GCCTGGTGCTCGCGGCGGTCCCGGCCGCCGTCATGACCGCCGGCGCGCTGTTCCTCCCGGAGACGCCCAACTCCCTCCTG
GAGCGCGGGAGGCGCGGCGAGGCCAGGCGGATGCTCCAGCGCGTGCGCGCCGAGGGCGTGGACGTGGAGGACGAGTACAA
CGACCTGGTCGCCGCCGGCGAGGCGTCCCGCGCCGTGGCGAGCCCGTGGCGCGACATCCTGCGGCGCCGCAACCGGCCGC
CGCTGGTGATGGCGGTGGCGATCCCGCTGTTCCAGCAGCTGACGGGCATCAACGTGATCATGTTCTACGCCCCGGTGCTG
TTCAGGACGCTGGGGTTCGGCGGCGGCGCGTCGCTGATGTCGGCTGTGATCACCGGCGGCGTGAACATGGCGGCGACGCT
GGTGTCCCTCCTCGCCGTGGACCGCGTGGGGCGGCGGGCGCTGTTCCTGGAGGGCGGCGCGCAGATGGTGGCGAGCCAGG
CGGCGGTGGGGGCGCTGATCGGGGCGAGGCTGGGGTGGTCGGGGACGGCGGCGATCCCGGCGGGGTACGCGGCGGCGGTG
GTGGCGGCCATGTGCGTGTACGTGGCGGCGTTCGCGTGGTCGTGGGGGCCATTGGCGTGGCTGGTGCCGAGCGAGGTGAT
GCCGCTGGAGGTGAGGCCGGCGGGGCAGAGCATCACGGTGGCGGTGAACATGGCCATGACGTTCGCCGTCGCGCAGGCGT
TCCTGCCGCTGCTCTGCCGCCTCAGGTTCGTGCTCTTCTTCTTCTTCGCCGGGTGGGTCGCCGCCATGACCGCCTTCGTC
GCGCTCTTCGTGCCCGAGACCAAGGGCGTCCCCATCGAGGACATGGCCGCCGTCTGGAGCGACCACTGGTACTGGAAGCG
CTTCGTCGACGGCGACGGCGCACGACGCCGAGGAGACATTGAGATGGGGCACAAGTAG

Alignment

ORF - retro_oglu_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.56 %
• Parental protein coverage: 96.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGVVVNNGGG---KDYPGKLTMFVLFACIVAATGGLIFGYDIGISGGVTSMNPFLIKFFPSVYRKEQ---
          GG..V..GGG.....YPG.LTMFV..AC.VAATGGLIFGYDIG.SGGVTSM.PFL..FFPSVYR......
Retrocopy GGAMVAAGGGGGRPEYPGGLTMFVSMACLVAATGGLIFGYDIGVSGGVTSMDPFLSRFFPSVYRAQSAAA

Parental  -AAEKNQSNQYCKFDSPLLTMFTSSLYLAALVASFFASTVTRVAGRKWSMFGGGVTFLVGAALNGAAKNV
          .AA.....NQYC.FDSPLLTMFTSSLYLAAL..S..A.TVTRVAGRKWSMF.GG..FL.G.ALNGAA.NV
Retrocopy AAAGGGGGNQYCRFDSPLLTMFTSSLYLAALASSLGAATVTRVAGRKWSMFAGGLVFLAGCALNGAAANV

Parental  LMLILGRVLLGVGVGFANQSVPLYLSEMAPARLRGMLNIGFQLMITIGILCANLINYGTAKIKGGWGWRV
          .MLI.GRVLLGVG.GFANQSVP.YLSEMAPAR.RGMLN.GFQ.MIT.G.L.ANLINYGTA.I.GGWGWR.
Retrocopy AMLIVGRVLLGVGIGFANQSVPVYLSEMAPARMRGMLNNGFQMMITTGVLAANLINYGTARIAGGWGWRL

Parental  SLALAAVPAAIIAVGALFLPDTPNSLIDRGHTDAAKRMLRRVRGTD-DIEEEYNDLVAASEESKLVAHPW
          SL.LAAVPAA....GALFLP.TPNSL..RG....A.RML.RVR....D.E.EYNDLVAA.E.S..VA.PW
Retrocopy SLVLAAVPAAVMTAGALFLPETPNSLLERGRRGEARRMLQRVRAEGVDVEDEYNDLVAAGEASRAVASPW

Parental  RNILQRRYRPQLTMAIAIPLFQQLTGINVIMFYAPVLFKTLGFADDASLMSAVITGLVNVFATFVSIVTV
          R.IL.RR.RP.L.MA.AIPLFQQLTGINVIMFYAPVLF.TLGF...ASLMSAVITG.VN..AT.VS...V
Retrocopy RDILRRRNRPPLVMAVAIPLFQQLTGINVIMFYAPVLFRTLGFGGGASLMSAVITGGVNMAATLVSLLAV

Parental  DRLGRRKLFLQGGTQMLACQIVVGSLIGAKFGFSGVADIPKEYAAFVVLFICAYVAGFAWSWGPLGWLVP
          DR.GRR.LFL.GG.QM.A.Q..VG.LIGA..G.SG.A.IP..YAA.VV...C.YVA.FAWSWGPL.WLVP
Retrocopy DRVGRRALFLEGGAQMVASQAAVGALIGARLGWSGTAAIPAGYAAAVVAAMCVYVAAFAWSWGPLAWLVP

Parental  SEIFPLEIRSAGQSINVSVNMLFTFIIAQAFLPMLCRFKFILFFFFGAWVVIMTLFVAFFLPETKNVPIE
          SE..PLE.R.AGQSI.V.VNM..TF..AQAFLP.LCR..F.LFFFF..WV..MT.FVA.F.PETK.VPIE
Retrocopy SEVMPLEVRPAGQSITVAVNMAMTFAVAQAFLPLLCRLRFVLFFFFAGWVAAMTAFVALFVPETKGVPIE

Parental  EMVLVWKSHWYWGRFIRDEDVHVGADVEM
          .M..VW..HWYW.RF..........D.EM
Retrocopy DMAAVWSDHWYWKRFVDGDGARRRGDIEM

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_7 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 12 parental genes, and 13 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	OGLUM07G00430	1 retrocopy	retro_oglu_47,
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,