RetrogeneDB ID: retro_omer_8

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 8:4526927..4528475(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI08G04740
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI07G15470
• Aliases: None
• Description: None

Sequence

>retro_omer_8
ATGGCGGGCGGCGCGATGGTCCAGACGGTGGGCGGCAAGACGTACCCGGGGAAGATGACGGCGTTCGTGTTCTTCACCTG
CCTCGTCGCCTCCTCCGGCGGCCTTATCTTCGGCTACGACATCGGCATCTCCGGCGGCGTCACCTCCATGGACTCCTTCC
TCAGCGAGTTCTTCCCGTCGGTGTACGCGCAGGCGAAGGCGAGCAAGGACACCAACCAGTACTGCAAGTTCGACAGCCAG
CTGCTGACCCTCTTCACCTCGTCGCTGTACCTGGCGGCGCTGGCGACGTCGTTCGTGGCGGCGTGGGTCACCCGGGTGTT
CGGCCGGAAGTGGTCCATGTTCTGCGGCGGCGTCACGTTCCTCGCCGGCTCGGCGCTCAACGGCGCCGCCACCGACGTCA
TGATGCTCATCCTCGGCCGCATCCTCCTCGGCGTCGGCGTCGGCTTCGCCAACCAGTCCGTGCCGCTCTACCTGTCGGAG
ATGGCGCCGGCGAACCTCCGCGGGATGCTCAACATCGGCTTCCAGCTCATGACCACCATCGGCATCCTCTCCGCCAACCT
CATCAACTACGCGACGTCGAGCATCGAGGGAGGGTGGGGGTGGCGCATCGGGCTCGGCCTCGCCGGCGTGCCCGCGCTCA
TCATCACGCTCGGCGCGCTCGTCCTCCCGGACACCCCAAACTCCCTCATCGCCCGCGGCTACGCCGGCGACGCCAAGCGC
GTCCTCGTCAAGATCCGCGGCACCGACGACGTCCACGACGAGTACGACGACATGGTAGCGGCAAGCGAAGAAGCCGCCTC
GATCGAACACCCATGGCGGAACATCCTCCAGCGCAAGTACCGCCCGCAGCTCACCATCGCCATCCTCATCCCGTGCTTCC
AACAACTCACCGGCATCAACGTGATCATGTTCTACGCGCCGGTGCTCTTCCTCACCATCGGCTTCGCCGGCGACGCGTCG
CTCATGTCCGCGGTGATCACGGGCCTCGTCAACATGTTCGCCACCGTCGTCTCGATCGTCTCCGTGGACCGCCTCGGCCG
GCGCGTGCTGTTCCTCCAGGGCGGCACGCAGATGTTCATCTCCCAGGTGGTGGTGGGCACGCTGATCGCGCTCCAGTTCG
GCGTCGCCGGCGTGGGCGAGATGTCGCGGTCGTACGCGATCTTGCTCGTACTGTTCATCTGCCTGTACGTGGCCGGGTTC
GCGTGGTCGTGGGGGCCGCTGGGGTGGCTGGTGCCGAGCGAGGTGTTCGCGCTGGAGATCAGGTCGGCGGGGCAGAGCAT
CGCGGTGTGCGTCAACATGATGCTGACGTTCGTCATCGGGCAGGCGTTCCTCACCATGCTGTGCCACCTCAAGTTCGGCC
TCTTCTACTTCTTCGCGGGGTGGATGCTGGTCATGACCACCTTCGTCGCGCTCTTCCTGCCGGAGACCAAGGGGGTGCCC
ATCGAGGAGATGAACCACGTCTGGAGCCGGCACTGGTTCTGGGGCAGCTACGTCACCGCCCACGACGTCGCCGGAGGAGG
AGGAAACCGCAGAAGCCACAACGTCTAG

Alignment

ORF - retro_omer_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.05 %
• Parental protein coverage: 95.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGGVVVNNGTGKDYPGKLTMFVLFACIVAATGGLIFGYDIGISGGVTSMNPFLIKFFPSVYRKEQAAEK
          MAGG..V....GK.YPGK.T.FV.F.C.VA..GGLIFGYDIGISGGVTSM..FL..FFPSVY....A...
Retrocopy MAGGAMVQTVGGKTYPGKMTAFVFFTCLVASSGGLIFGYDIGISGGVTSMDSFLSEFFPSVYAQAKASK-

Parental  NQSNQYCKFDSPLLTMFTSSLYLAALVASFFASTVTRVAGRKWSMFGGGVTFLVGAALNGAAKNVLMLIL
          ...NQYCKFDS.LLT.FTSSLYLAAL..SF.A..VTRV.GRKWSMF.GGVTFL.G.ALNGAA..V.MLIL
Retrocopy -DTNQYCKFDSQLLTLFTSSLYLAALATSFVAAWVTRVFGRKWSMFCGGVTFLAGSALNGAATDVMMLIL

Parental  GRVLLGVGVGFANQSVPLYLSEMAPARLRGMLNIGFQLMITIGILCANLINYGTAKIKGGWGWRVSLALA
          GR.LLGVGVGFANQSVPLYLSEMAPA.LRGMLNIGFQLM.TIGIL.ANLINY.T..I.GGWGWR..L.LA
Retrocopy GRILLGVGVGFANQSVPLYLSEMAPANLRGMLNIGFQLMTTIGILSANLINYATSSIEGGWGWRIGLGLA

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

Parental  RYRPQLTMAIAIPLFQQLTGINVIMFYAPVLFKTLGFADDASLMSAVITGLVNVFATFVSIVTVDRLGRR
          .YRPQLT.AI.IP.FQQLTGINVIMFYAPVLF.T.GFA.DASLMSAVITGLVN.FAT.VSIV.VDRLGRR
Retrocopy KYRPQLTIAILIPCFQQLTGINVIMFYAPVLFLTIGFAGDASLMSAVITGLVNMFATVVSIVSVDRLGRR

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

Parental  EIRSAGQSINVSVNMLFTFIIAQAFLPMLCRFKFILFFFFGAWVVIMTLFVAFFLPETKNVPIEEMVLVW
          EIRSAGQSI.V.VNM..TF.I.QAFL.MLC..KF.LF.FF..W...MT.FVA.FLPETK.VPIEEM..VW
Retrocopy EIRSAGQSIAVCVNMMLTFVIGQAFLTMLCHLKFGLFYFFAGWMLVMTTFVALFLPETKGVPIEEMNHVW

Parental  KSHWYWGRFIRDEDVHVG
          ..HW.WG......DV..G
Retrocopy SRHWFWGSYVTAHDVAGG

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza meridionalis was not studied using ChIP-Seq data.

EST

Oryza meridionalis was not studied using EST data.

TSS

Oryza meridionalis was not studied using FANTOM5 data.

Lab

retro_omer_8 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza meridionalis 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,