RetrogeneDB ID: retro_hvul_4

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:525258730..525262552(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_37065
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_10099
• Aliases: None
• Description: None

Sequence

>retro_hvul_4
ATGACCGAGTTCATCTGCCCCAAATGCCGCATGGCGCAGCGCCTCCCCCCGCAGCTCATGCCCTACTCCTCCCCGCCCAA
GGCGTCCCCTACCCCGCCTCCGCCCCAGCCTCCTCCCCTTCCTCCTCACCCTCAGTCTCAGCCCGCGCCTCCCGCTCCCG
CTCTCCCCGCCGCTTCCCGCCGCTCTGGGCCGCGGGCGCAGGGCGTGGACCCCACCAAGATCCAGCTGCCCTGCGCGCGC
TGCAAGGCCATCCTCAACGTGCCGCACGGCCTCGCCCGCTTCCGCTGCCCGCAGTGCGACGTCGACCTCGCCGTCGACAT
CTCCAAGCTCCAGCATTTCCTTACCGCCGCCGCCCCTGGGCCTGGCTTCGTTCCTCCACCGCCTCCGCCCGCGCCTCCGC
TCCCAATGCCGCACATGCCCTTCCTGCCGATGATGCCGCCCCCGCGCATGCCGATGCCCCCAATGGTCCCGCCACCCGAG
CCGCCGGAGGAGATCAACGAGGTTGCGCTTGACGTTGAACGCGAGGAAGATGAAGGTGACACTGTTGGTGAAACTTTCAT
GGACTACAGGCCTCCTAAGCTGTCTCTTGGTCTTCCTCATCCGGATCCTGTGGTGGAGACTTCATCTTTATCAGCTGTGC
AGCCTCCTGAGCCTACTTACAACTTGGCTATCATGGATGAATTGGATGAGACCAGGGCATTGTCATGCTTACAGATTGAG
ACAATTGTGTATGCTTGTCAGAGGCATCTTCATCATCTCCCTACTGGTGCTAGAGCAGGTTTCTTCATTGGTGATGGAGC
CGGTGTTGGTAAAGGGCGTACAATTGCTGGATTGATTTGGGAGAATTGGCAACAGGGGAGGCATAAGGCATTGTGGATTT
CCATTGGTTCAGACTTGAAATATGATGCCCGCAGAGATTTGGATGATGTTGGTGCAAAATGTGTGCAAGTGCACGCGTTG
AACAAGCTGCCATATTCTAAGTTAGACTCGAAGGCCACTGGGATCACAGACGGAGTTGTTTTTGTAACTTATAGCAGTTT
AATAGCATCTTCTGAGAAAGGACATTCACGGTTGCGGCAGCTGGTAGAGTGGTGTGGATCTGAGTTCGAAGGTCTTGTGG
TGTTTGATGAGTGCCACAAGGCTAAAAATCTGATTCCTGAGGCAGGAGGTCAGCCCACACGCACTGGTAAATCAGTTCTT
GAGATCCAAGACATGTTACCTGAAGCTCGAGTGGTTTACTGCTCAGCAACTGGTGCATCAGAGCCTCGGAATTTAGGCTA
CATGGTCCGGCTTGGTCTCTGGGGAGACGGAACATCATTTCAGAGTTTTCACCAATTTTTAGGTGCTCTTGAGAAAGGTG
GTGTGGGTGCCCTTGAACTTGTTGCTATGGACATGAAAGCTAGGGGTATGTATGTTTGCCGCACACTAAGTTATAAGGGT
GTTGATTTTGATGTTGTGGAGGCACCTCTAGAGGACAGAATGATGAATATGTATAGAAAGGCAGCTGAATTTTGGGCTGA
GTTGCGTGTTGAGCTCCTATCGGCAAGTGAGTACTATGCAGAAGACAAGGGCAATTCAGCTCACATATGGCGGTTATACT
GGGCCAGCCATCAGCGTTTCTTTAGGCATATGTGTATGTCTGCAAAGGTACCTGCTGTTGTGAGGTTGGTGAAGGAAGCC
TTAGCAGAAGAAAGATGTGTGGTGGTTGGTCTCCAGAGCACTGGTGAAGCTCGAACAGAGGAAGCTATCACAAAATATGG
TCTTGAAATGGAAGACTTTATTTCTGGTCCTAGAGAGTTGCTTCTTAAGCTGGTAGAAGATAACTATCCCTTGCCTCCAA
AACCCGATTGTTCTCAGCAAGGTGAAGAAAAGGTTATGGAGGTCCAGCGTAAGCGACCCGATGTATCCTCAAAAGGACGA
GTTAGGAAACTCACAAAAATGGAAGATAGTGATGATGGAATAGATGCGCACTATCCGTTGGAGTCAGACCATGAATTAAC
AGATTCTGAAGAGGAATTGCATATGTGTCAGATCTGCAATACCGAGGAGGAGAAGAGCCTGTTGCTTCATTGTTCCAATT
GTGCTACAAGTGTTCACCCTGGCTGTCCAATTCCACCATGGACTGGAACGTTGACAGATGATTGGTTATGTTATGCATGC
AAGGAGATAATAGAAGGCTATTTTAAAGAGAGGGATGCTTACATGGCTGAACTATCAAAGAGATATGACAATGCAGTGGA
CAGGAAGTCAAAGATTTTAGAAATCATCCGTGCTTTAGATTTGCCTAATAATCCTCTAGATGATATCATTGATCAGCTAG
GTGGTCCAGACAATGTTGCAGAAATAACTGGAAGGCGTGGTATGCTAATAAGAGCATCAGATGGAAAAGGTGTTGTTTAC
CAGGCACGGAACACGAAAGAAATTGCATTTGACATGATCAATATGCATGAAAAGCAGCTATTCATGGACGGAGAAAAGTT
TATCGCAATAATATCGGAAGCAGGATCAGCTGGTGTTTCCTTACATGCTGATCGAAGGGTTAAAAATCAGAGAAGAAGAG
TACACATAACACTTGAACTTCCATGGAGTGCAGACCGTGCAACCCAGCAGTTTGGGAGAACACATCGTTCTAATCAAACT
TCTGCACCTGTATATAGGATTCTTTTTACCAACCTTGGTGGTGAAAAGCGATTTGCATCAATTGTGGCAAAGCGACTAGA
GTCTCTTGGAGCTTTAACACAAGGAGATCGAAGAGCTGGACCATCACTTAGTGCTTTTAACTATGACAGCAGTTATGGGA
AAAAAGCCCTGACAATGATGTACAGGGGTATAATGGAACAGGATGCATTTCCAGTTGTGCCTTTGGGATGCTCGGAGAAT
CAATCTAGTCTCCAAGAATTCATCACTAGATCAAAAGCTGCGTTAGTGGCAGTTGGAATTGTCAGGGATGCTGTAATCTG
CATTGGAAAACATGGAGCAAAGCTTACTGGTAGAATTGTTGATTCTGATATGCATGATGTGGCCCGTTTCCTCAACCGTA
TTCTGGGATTAGCTCCAAACATCCAGAATGGGTTATTTGATCTCTTCACAAGCATACTCGACGTGGTAATTCAGAATGCA
CGAAGCGAAGGACAGCTTGATTCTGGTATTGTTGATATTAAAGCAAAAAGGGTTGAAATGAAAGAACCGCCGAAGACAGT
TCATGTTGATAGCCTGTCCGGTGCTTCCACGGTGTTGTTCACTCTTACAATTGACCGTGGAGTTACTTGGGAGTCAGCAA
ATGCAATGCTTGAAGAAAGGCAGAAAGATGGTGCATGCTCTTCTAATGACGGGTTTTACGAGTCCAGGAGGGAATGGATG
GGCAGAAGACATTTCATGCTAGCGTTTGAAGGCTCAACGGAAAGAATGTACAGAGTAACTCGCCCTGCCGTCGGGGAAGC
TTCGAAGGAGATGCCTTTGGCTGAACTAGAAGGAAAGTACAAGAAGGTCTCATCGGCTGACAAAACTGGGGAAGGCTGGC
AGGAAGAATACGATGTGTCGTCCAAGCAGTGCATGCATGGGCCCAAGTGCAGACTTGGAAGCGATTGTACTGTGGGCAGA
AGGTTACAAGAGATTAATGTTTTGGGTGGTCTAATACTTCCTGTGTGGGGTGCAGTAGAAAAGGCCCTGAATAAGCAGGC
CCGACAGGCTCACAAGAGGATACGTGTCGTCCGCCTGGAGACAACAGATGACAACCATCGGATTGTTGGGCTTGTCATTC
CAAACGCAGCAGTGGAGTCGGTGTTAGAAGGTCTGCAGTGGGTCCAGGACATCGATGAATGA

Alignment

ORF - retro_hvul_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.72 %
• Parental protein coverage: 97.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPTFLPVLPPGMPQPPQLVAVTTTVPIGLPATEPPEEINEVAVDVERDEDEGGTVGETFTDYRPPKLSLG
          PP...P...P.MP..P.........P...P..EPPEEINEVA.DVER.EDEG.TVGETF.DYRPPKLSLG
Retrocopy PPPAPPLPMPHMPFLPMMPPPRMPMPPMVPPPEPPEEINEVALDVEREEDEGDTVGETFMDYRPPKLSLG

Parental  LPHPDPVVETSSLSAVQPPEPTYELTIMDELDQTKTLSCLQIESIVYASQRHLHHLPTGDRAGFFIGDGA
          LPHPDPVVETSSLSAVQPPEPTY.L.IMDELD.T..LSCLQIE.IVYA.QRHLHHLPTG.RAGFFIGDGA
Retrocopy LPHPDPVVETSSLSAVQPPEPTYNLAIMDELDETRALSCLQIETIVYACQRHLHHLPTGARAGFFIGDGA

Parental  GVGKGRTIAGLIWENWQQGRHKAVWVSVGSDLKYDARRDLDDVGAKCVQVHPLNKLPYSKLDSKAIGIKN
          GVGKGRTIAGLIWENWQQGRHKA.W.S.GSDLKYDARRDLDDVGAKCVQVH.LNKLPYSKLDSKA.GI..
Retrocopy GVGKGRTIAGLIWENWQQGRHKALWISIGSDLKYDARRDLDDVGAKCVQVHALNKLPYSKLDSKATGITD

Parental  GVIFVTYSSLIASSERGRSRLQQLVQWCGHEFDGLIVFDECHKAKNLIPDAGSQPTRTGKAVLEIQEKLP
          GV.FVTYSSLIASSE.G.SRL.QLV.WCG.EF.GL.VFDECHKAKNLIP.AG.QPTRTGK.VLEIQ..LP
Retrocopy GVVFVTYSSLIASSEKGHSRLRQLVEWCGSEFEGLVVFDECHKAKNLIPEAGGQPTRTGKSVLEIQDMLP

Parental  EARVVYCSATGASEPRNLGYMVRLGLWGDGTSFQDFPQFLGALEKGGVGALELVAMDMKARGMYVCRTLS
          EARVVYCSATGASEPRNLGYMVRLGLWGDGTSFQ.F.QFLGALEKGGVGALELVAMDMKARGMYVCRTLS
Retrocopy EARVVYCSATGASEPRNLGYMVRLGLWGDGTSFQSFHQFLGALEKGGVGALELVAMDMKARGMYVCRTLS

Parental  YKGADFDTVEAPLEERMMNMYGKAAEFWAELRLELLSAGEISGEEKGISNQIWRLYWASHQRFFRHMCMS
          YKG.DFD.VEAPLE.RMMNMY.KAAEFWAELR.ELLSA.E...E.KG.S..IWRLYWASHQRFFRHMCMS
Retrocopy YKGVDFDVVEAPLEDRMMNMYRKAAEFWAELRVELLSASEYYAEDKGNSAHIWRLYWASHQRFFRHMCMS

Parental  AKVPAVVKLAKEALAENKCVVIGLQSTGEARTEEAVTKYGVEMEDFVSGPRELLLKLVEENYPLPPKPDS
          AKVPAVV.L.KEALAE..CVV.GLQSTGEARTEEA.TKYG.EMEDF.SGPRELLLKLVE.NYPLPPKPD.
Retrocopy AKVPAVVRLVKEALAEERCVVVGLQSTGEARTEEAITKYGLEMEDFISGPRELLLKLVEDNYPLPPKPDC

Parental  FQQGEEKVTEIQRKRHSAPDVSFKGRVRKVAKMEEVSDDDSDDYSPSESSDHESTESDEEFHMCQICNSE
          .QQGEEKV.E.QRKR...PDVS.KGRVRK..KME..SDD..D...P.E.SDHE.T.S.EE.HMCQICN.E
Retrocopy SQQGEEKVMEVQRKR---PDVSSKGRVRKLTKMED-SDDGIDAHYPLE-SDHELTDSEEELHMCQICNTE

Parental  EEKSLLLNCSGCSLRVHPSCLTPPWTGMLTDDWSCYSCKK-IEGQEMEHDANIADFSKRYVSAVESKLKI
          EEKSLLL.CS.C...VHP.C..PPWTG.LTDDW.CY.CK..IEG...E.DA..A..SKRY..AV..K.KI
Retrocopy EEKSLLLHCSNCATSVHPGCPIPPWTGTLTDDWLCYACKEIIEGYFKERDAYMAELSKRYDNAVDRKSKI

Parental  LDIIRSLDLPNNPLDDIIDQV
          L.IIR.LDLPNNPLDDIIDQ.
Retrocopy LEIIRALDLPNNPLDDIIDQL

Legend:

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

Expression

RNA-Seq

Hordeum vulgare was not studied using RNA-Seq expression data.

ChIP-Seq

Hordeum vulgare was not studied using ChIP-Seq data.

EST

Hordeum vulgare was not studied using EST data.

TSS

Hordeum vulgare was not studied using FANTOM5 data.

Lab

retro_hvul_4 was not experimentally validated.

Homology

Retrocopy orthology:

Hordeum vulgare 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
Hordeum vulgare	MLOC_10099	1 retrocopy	retro_hvul_4 ,