RetrogeneDB ID: retro_omer_19

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 7:26683104..26684874(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI07G23820
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI02G33690
• Aliases: None
• Description: None

Sequence

>retro_omer_19
ATGGAGAGCAACGGCGGAGGAGGAGGATCTCCCAAGGAGGCAGCGGTGGTGGTGCCGTCCTCCGGCGACGCCACACTGGG
CGGCCACCTGGCGCGGCGCCTCGTGCAGGTGGGCGTGAGCGACGTGTTCGCCGTGCCCGGGGACTTCAACCTGACGCTTC
TGGACCACCTCATCGCCGAGCCGGGGCTCCGCGTCGTGGGCTGCTGCAACGAGCTGAACGCCGGGTACGCCGCCGACGGG
TACGCGCGGGCCCGTGGCGTGGGCGCCTGCGCCGTGACCTTCACCGTGGGCGGGCTGAGCGTGCTGAACGCCATCGGCGG
CGCGTACAGCGAGAACCTGCCGCTGATCTGCATCGTGGGGGGCCCAAACTCCAACGACTACGGCACCAACCGCATCCTCC
ACCACACCATCGGCCTCCCGGACTTCTCCCAGGAGCTCCGCTGCTTCCAGCCCCTCACCTGCTACCAGGCCGTCGTCAGC
AACCTCGACGACGCCCACGAGCAGATCGACCGCGCCATCTCCACCGCCATCAGGGAAAGCAAGCCCGTCTACATCAGCGT
CAGCTGCAACCTCCCCGCCGTCCCCCACCCCACCTTCTCCCGCGACCCGGTGCCCTACTTCCTCTCCCCGAGGCTCTCCA
ACCAGGCCAGCCTCCACGCCGCGCTCGACGCCACCCTCGCCTTCCTCGACAAGGCCGTCAAGCCCGTCCTCGTCGCGGGG
CCCAAGCTCCGCGTGGCCAAGGCCGGAGGGGCCTTCGTGGACCTCGCCGACGCCAGCGGCTACGCGGTGGCCGCCATGCC
GTCCGCCAAGGGGCTGGTGCCGGAGACGCTGCCGCGCTTCATCGGGACCTACTGGGGCGCGGTCAGCACGGCGTTCTGCG
CGGAGATCGTGGAGTCCGGGGACGCCTACCTGTTCGCGGGGCCCATCTTCAACGACTACAGCTCCGTGGGGTACTCGTGC
CTGCTGAAGAAGGACAAGGCGGTGGTGGTGCAGCCCGACCGCGTGACCATCGGCAATGGCCCCGCGTTCGGGTGCGTGAT
GATGAGGGACTTTCTGTCGGAGCTGGCCAAGCGCGTCCGGAAGAACACGACGGCGTTCGACAACTACAAGAGGATCTTCG
TGCCGGAGGGGCAGCTGCCGGAGTGCGAGGCCGGCGAGGCGCTGCGGGTGAACGTGCTGTTCAAGCACATACAGAGGATG
ATCGGTGGCGCGGAGATCGGGGCGGTGATGGCGGAGACGGGGGACTCGTGGTTCAACTGCCAGAAGCTGCGGCTGCCCGA
GGGTTGCGGGTACGAGTTCCAGATGCAGTACGGCTCCATCGGGTGGTCGGTGGGGGCGCTGCTGGGCTACGCGCAGGCTC
TCGGACAAGATAAGCGGGTGGTCGCCTGCATCGGCGACGGCAGCTTCCAGGTGACGGCGCAGGACGTGTCGACGATGCTG
CGGTGCGGGCAGCGGAGCATCATCTTCCTCATCAACAACGGCGGGTACACCATCGAGGTGGAGATCCACGACGGGCCGTA
CAACGTGATCAAGAACTGGGACTACGTGGGCCTCGTCAACGCCATCCACAACGGCGAGGGGCGGTGCTGGGCCACACGGG
TGCGGTGCGAGGAGGAGCTGGAGGCGGCCATCGCGACGGCCACGGGGGACAAGGCGGACAGCCTCTGCTTCATCGAGGTG
GTGGCGCACAAGGACGACACCAGCAAGGAGCTCCTCGAATGGGGCTCCAGGGTCTCCGCCGCCAACTCCAGGCCGCCCAA
CCCGCAGTAG

Alignment

ORF - retro_omer_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.16 %
• Parental protein coverage: 95.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCPMTSARPAPVSAGEASLGRHLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLRLVGCCNELNAGYA
          G.P...A...P.S.G.A.LG.HLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLR.VGCCNELNAGYA
Retrocopy GSPKEAAVVVP-SSGDATLGGHLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLRVVGCCNELNAGYA

Parental  ADGYARARGVGACAVTFTVGGLSVLNAIAGAYSENLPVICIAGGPNSNDYGTNRILHHTIGLPDFSQELR
          ADGYARARGVGACAVTFTVGGLSVLNAI.GAYSENLP.ICI.GGPNSNDYGTNRILHHTIGLPDFSQELR
Retrocopy ADGYARARGVGACAVTFTVGGLSVLNAIGGAYSENLPLICIVGGPNSNDYGTNRILHHTIGLPDFSQELR

Parental  CFQTVTCHQAVVTNLEDAHEQIDTAIATALRESKPVYLSISCNLPGLPHPTFSRDPVPFFLSPRLSNKMG
          CFQ..TC.QAVV.NL.DAHEQID.AI.TA.RESKPVY.S.SCNLP..PHPTFSRDPVP.FLSPRLSN...
Retrocopy CFQPLTCYQAVVSNLDDAHEQIDRAISTAIRESKPVYISVSCNLPAVPHPTFSRDPVPYFLSPRLSNQAS

Parental  LEAAVEATVEFLNKAVKPVLVGGPKLRVAKAGKAFVDLVDASGYAYAVMPSAKGLVPETHPHFIGTYWGA
          L.AA..AT..FL.KAVKPVLV.GPKLRVAKAG.AFVDL.DASGYA.A.MPSAKGLVPET.P.FIGTYWGA
Retrocopy LHAALDATLAFLDKAVKPVLVAGPKLRVAKAGGAFVDLADASGYAVAAMPSAKGLVPETLPRFIGTYWGA

Parental  VSTAFCAEIVESADAYLFAGPIFNDYSSVGYSFLLKKDKAIIVQPERVIVGNGPAFGCVMMKEFLSELAK
          VSTAFCAEIVES.DAYLFAGPIFNDYSSVGYS.LLKKDKA..VQP.RV..GNGPAFGCVMM..FLSELAK
Retrocopy VSTAFCAEIVESGDAYLFAGPIFNDYSSVGYSCLLKKDKAVVVQPDRVTIGNGPAFGCVMMRDFLSELAK

Parental  RVNKNTTAYENYKRIFVPEGQPLESEPNEPLRVNVLFKHVQKMLNSD--SAVIAETGDSWFNCQKLKLPE
          RV.KNTTA..NYKRIFVPEGQ..E.E..E.LRVNVLFKH.Q.M.......AV.AETGDSWFNCQKL.LPE
Retrocopy RVRKNTTAFDNYKRIFVPEGQLPECEAGEALRVNVLFKHIQRMIGGAEIGAVMAETGDSWFNCQKLRLPE

Parental  GCGYEFQMQYGSIGWSVGALLGYAQG-AKDKRVIACIGDGSFQVTAQDVSTMIRCAQNSIIFLINNGGYT
          GCGYEFQMQYGSIGWSVGALLGYAQ....DKRV.ACIGDGSFQVTAQDVSTM.RC.Q.SIIFLINNGGYT
Retrocopy GCGYEFQMQYGSIGWSVGALLGYAQALGQDKRVVACIGDGSFQVTAQDVSTMLRCGQRSIIFLINNGGYT

Parental  IEVEIHDGPYNVIKNWNYTGLVDAIHNGEGKCWTSKVKCEEELTEAIAMALGEKKDCLCFIEVIAHKDDT
          IEVEIHDGPYNVIKNW.Y.GLV.AIHNGEG.CW...V.CEEEL..AIA.A.G.K.D.LCFIEV.AHKDDT
Retrocopy IEVEIHDGPYNVIKNWDYVGLVNAIHNGEGRCWATRVRCEEELEAAIATATGDKADSLCFIEVVAHKDDT

Parental  SKELLEWGSRVSAANSRPPNPQ
          SKELLEWGSRVSAANSRPPNPQ
Retrocopy SKELLEWGSRVSAANSRPPNPQ

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_19 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G087186	1 retrocopy	retro_zmay_12,
Oryza barthii	OBART03G13620	1 retrocopy	retro_obar_6,
Oryza glumaepatula	OGLUM03G13720	1 retrocopy	retro_oglu_28,
Oryza meridionalis	OMERI02G33690	1 retrocopy	retro_omer_19 ,
Oryza punctata	OPUNC03G13130	1 retrocopy	retro_opun_18,
Oryza rufipogon	ORUFI03G14280	1 retrocopy	retro_oruf_25,