RetrogeneDB ID: retro_obra_1

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 2:527618..529691(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB02G11010
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB02G11000
• Aliases: None
• Description: None

Sequence

>retro_obra_1
ATGGCGGAGGCGGAGGCGGCGGCGGCGGCGTTGCGGGAGGTGATATCGACGGAGAAGGCGTTCGAGGGGAAGGCGCTGCC
GGCGTGGTCGGAGCAGATAACGGTGAGGTCGGTGGTGGTGAGCGCGGTGCTGGGGCTGTTCCTGAGCTTCATCGTGATGA
AGCTGAACCTGACGTCGGGGATCGTGCCGTCGCTGAACATCTCGGCGGGGCTGCTCGCCTTCTTCCTCATGAAGACGTGG
ACGAGCGCGCTGGAGCGGTGCGGCGTCTTCCCGCGGCCCTTCACCCGCCAGGAGAACACCGTGGTGCAGACCTGCGTCAT
CTCCTGCTCCAGCATCGCCTTCTCCGGCGGCTTCGGCACCTACATCCTGGGGATGAGCAAGAGCATCGCCGAGGGCTTCG
ACGAGGCCAAGACCAGCATCAACGTCGAGGAGCCGTCGCTGGGGCGCATCATCGCCTTCCTCTTCCTCGTCAGCTTCGTG
GGGCTCTTCTCCATCGTCCCGCTCCGCAAGATCATGATCATCAGCTACAAGCTCACCTACCCCAGCGGCTCCGCCACCGC
GCACCTCATCAACAGCTTCCACACGCCGCAGGGCGCCATCCAGGCCAAGCGCCAGGTCTCCATCCTCTTCAAGTCCTTCG
TCGGAAGCTTCTTCTGGTCGCTCTTCCAGTGGTTCTTCGCCTCCGCCCCCGGCTGCGGCTTCAGCTCCTTCCCCACCTTC
GGCCTCGCCGCCTACAGCCGCCGCTTCTACTTCGACTTCTCCGCCACCTACGTCGGCGTCGGCATGATCTGCCCCTACAT
CATCAACTTCTCGCTGCTCATCGGCTCCGTCGTCTCCTGGGGGATCATGTGGCCGTACATCGAGAGCAAGAAGGGGACGT
GGTACGACGCGCGCCTCCCCAAGAGCAGCCTCCATGGCCTCAACGGCTACCAGGTCTTCATCTCCATCGCCATGATCGTC
GGCGACGGCCTCTTCAACTTCTTCTCCATCGTCATGCGCACCGCCTACGACATGTACCTCAAGCGCCGCGGCGGAGGCGC
CGGCGCCGGGAACAGGCAGCAGGAGCAGCTGTTCGCCGGCGCCACGGGCACCGAGCGGCAGGCGCTGAGCTTCGACGACC
GGCGGCGGACGCAGGTGTTCCTCAAGGACCAGATCCCGACGTCGATCGCGGCGGCGGCGTACGTGCTCCTCGCCGCCATC
TCGGTGGTGGCCATCCCGCACATCTTCCGGCAGCTGCGGCCGAAGCACGTGGTGTGGGCGTACGTGGTGGCGCCGCTCTT
CGCCTTCTGCAACGCCTACGGCACCGGCCTCACCGACTGGTCGCTCTCCAGCAGCTACGGCAAGCTCGCCATCTTCATCT
TCGGCGCCAACATCGGCGCCCGCGACGGCGGCGTGGTGGCCGGGCTCGCCGCCTGCGGGCTCATGATGGGCATCGTCTCC
ACGGCGTCCGACCTGGTCCAGGACTTCAAGACCGGGTACCTCACCCTGACCTCGCCGCGGTCCATGTTCGTGAGCCAGGT
GATGGGCACCGGGCTGGGCTGCATCATCAGCCCCATGGTGTTCTGGATCTTCTACAAGGCGAACAACATCGGGGTGGACG
AGAACTTCCCGGCGCCGTACGCGAAGATCTACCGGGGGATCGCGCTGCTCGGCGTCAATGGCTGGGACCAGCTCCCGCGC
TACTGCCTCCGCTTCTGCCTCGCCTTCTTCCTCCTGGCCATCGCCATCTGCACGCTCAAGGAGGTGGCGAAGCAGCGGCG
GTGGTGGATCCAGGACTACATCCCCAGCGCGCTCGGCATGGCCGTGCCCTTCTTCCTCGGCTCCTTCTTCACCATCGACA
TGTGCGTCGGCAGCCTGGTGCTCTACCTCTGGTCCCGCGCCGACCCGCTCCGCGCCCAGACCTTCGCCCCCGCCGTCGCC
TCCGGCCTCATCTGCGGCGACGGCATCTGGTCGCTGCCCTCCTCCATCCTCTCGCTCGCCAACGTCAGCCCGCCCATGTG
CATGCGCGTCTTCTCCGCCGCCACCAACGAGAAGGTCCAGCTCTTCCTCAGGACGCTCCCCGTGCTGCCATGA

Alignment

ORF - retro_obra_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.08 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQEDISTEHAFEAEPVPSLSETITPRSLVFSFIIGATLSVVAMKVTLSSGFILSLSIPAGLLGFYVSRAW
          L.E.ISTE.AFE....P..SE.IT.RS.V.S...G..LS...MK..L.SG...SL.I.AGLL.F.....W
Retrocopy LREVISTEKAFEGKALPAWSEQITVRSVVVSAVLGLFLSFIVMKLNLTSGIVPSLNISAGLLAFFLMKTW

Parental  IRILDYFAVSHLPFTRQENTIIQTCVVACTSVTFTGGFGTYILAMSKKAAGG--DVKDDNNIEEPSIAKM
          ...L....V...PFTRQENT..QTCV..C.S..F.GGFGTYIL.MSK..A.G....K...N.EEPS....
Retrocopy TSALERCGVFPRPFTRQENTVVQTCVISCSSIAFSGGFGTYILGMSKSIAEGFDEAKTSINVEEPSLGRI

Parental  ITFLFLISFAGMFIIMPFRKIMIIRHRLTYPSGTATAHLINSFHTPQGVKQARNQVTLLFKSFGGTMAWS
          I.FLFL.SF.G.F.I.P.RKIMII...LTYPSG.ATAHLINSFHTPQG..QA..QV..LFKSF.G...WS
Retrocopy IAFLFLVSFVGLFSIVPLRKIMIISYKLTYPSGSATAHLINSFHTPQGAIQAKRQVSILFKSFVGSFFWS

Parental  FFQWFFASGPGCGFKFFPTFGLEAYKHGFFFDFSMANVGIGMMCPYMIVFSMLIGSIISWCMIWPYIQTK
          .FQWFFAS.PGCGF..FPTFGL.AY...F.FDFS...VG.GM.CPY.I.FS.LIGS..SW...WPYI..K
Retrocopy LFQWFFASAPGCGFSSFPTFGLAAYSRRFYFDFSATYVGVGMICPYIINFSLLIGSVVSWGIMWPYIESK

Parental  EGIWYPSNLGPDSLSGIRGYKVLIGLSMILADCLFVFLSIMVRTACAMVKRRQQASHGVGGGGGGCNMQQ
          .G.WY...L...SL.G..GY.V.I...MI..D.LF.F.SI..RTA..M...R.....G.G.G.G.....Q
Retrocopy KGTWYDARLPKSSLHGLNGYQVFISIAMIVGDGLFNFFSIVMRTAYDMYLKRR----GGGAGAGNRQQEQ

Parental  PFQCLDATDRPARSFDDRRRAQVFLRDEIPNSVAIGCYVLLSVVSIVAIPLLYPQLRYHHVALIYLAAPI
          .F.....T.R.A.SFDDRRR.QVFL.D.IP.S.A...YVLL...S.VAIP....QLR..HV...Y..AP.
Retrocopy LFAGATGTERQALSFDDRRRTQVFLKDQIPTSIAAAAYVLLAAISVVAIPHIFRQLRPKHVVWAYVVAPL

Parental  FAFCNAYGCGVTDINLGSTYCKIAMLVFGSWIGVKGGGVIAALVAGGIMVSILGTAADLTQDLKTGYLTL
          FAFCNAYG.G.TD..L.S.Y.K.A...FG..IG...GGV.A.L.A.G.M..I..TA.DL.QD.KTGYLTL
Retrocopy FAFCNAYGTGLTDWSLSSSYGKLAIFIFGANIGARDGGVVAGLAACGLMMGIVSTASDLVQDFKTGYLTL

Parental  TSPRAVFISEVIGMTLGCIINPTVFWAFYKMNPSAAGGDMSDTPYAKLYRGFAMLSV-GEEGLPGHSMFL
          TSPR..F.S.V.G..LGCII.P.VFW.FYK.N...........PYAK.YRG.A.L.V.G...LP......
Retrocopy TSPRSMFVSQVMGTGLGCIISPMVFWIFYKAN-NIGVDENFPAPYAKIYRGIALLGVNGWDQLPRYCLRF

Parental  CKLFFALAMALSAVREVANRKQWRVRRYIPSTIGMAVAFIMPPRMPVGMAVGSLVAYLWEKADAARGRML
          C..FF.LA.A.....EVA....W....YIPS..GMAV.F.........M.VGSLV.YLW..AD..R....
Retrocopy CLAFFLLAIAICTLKEVAKQRRWWIQDYIPSALGMAVPFFLGSFFTIDMCVGSLVLYLWSRADPLRAQTF

Parental  SPAMASGFICGDGLGSLLLSTLTLVHATAPICIKFLARGDNDRLDAFLATLP
          .PA.ASG.ICGDG..SL..S.L.L.....P.C........N.....FL.TLP
Retrocopy APAVASGLICGDGIWSLPSSILSLANVSPPMCMRVFSAATNEKVQLFLRTLP

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza brachyantha was not studied using ChIP-Seq data.

EST

Oryza brachyantha was not studied using EST data.

TSS

Oryza brachyantha was not studied using FANTOM5 data.

Lab

retro_obra_1 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza brachyantha 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB02G11000	1 retrocopy	retro_obra_1 ,