RetrogeneDB ID: retro_hvul_59

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:384284920..384286156(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_76416
• Aliases: None
• Description: None

Sequence

>retro_hvul_59
AAGAAGGCGGCGAACCGGCTGGTGGTGGAGGATGCCAGCACCAACGACGACAACTCCGTGTGCACCCTCCACCCAGACAC
CATGGAGAAGCTTTCCCTATTCAAGGGCGACACGGTGCTGCTCAAGGGCAAGCGCCGCCACAGCACGGTCTGCATGGCAC
TGCCCGACGACACCTGCGAGGAGCACAAGATGAGGATCAACAAGGTGGCCCGCTCCAACCTGCGCGTGCGCATCGCCGAC
GTCGTGTCCGTGCACCTGTGCCACGACGTCAAGTACGCCAGGCGCGTGCACATCCTCCCGTTGGACGACACCGTCGAGGG
CATCGCGGGGAACCTCTTCGACGCCTACCTCAAGCCCTACTTCGTGGACGCCTTCCGCCCGGTCCACAAGGGCGACCTCT
TCCTCGTGCGCGGCGGCATGCGGAGCGTCGAGTTCAAGGTCATGGAGATCGACCCCGCGGCGGACTACTGCATCGTGATG
CCCGACACGGAGATTTTCTGCGAGGGCGAGCCGGTCAAGCGGGAGGACGAGGAGCGGCTCGACGACGTCGGCTACGACGA
CGTGGGTGGCATGGGGAAACCGCTGACTCAGATCAGGGAGCTCGTCGAGCTGCCACTCAGGCATCCTCAGATCTTCAAGT
CCATTGGCGTCAAGCCTCCCAAGGGCATCCTCCTCTACGGCCCTCCCGGTTCCGGCAAGACGCTGATCGCCCGCGCGGTG
GCCAACGAGACCGGGGCCTTCTTCTTTCTCATCAACGGCCCGGAGATAATGTCAAAGATGGCCGGAGAGAGCGAGAGCAA
CCTGAGGAAGGCCTTCGAGGAGGCCGAGAAGAACGCGCCCTCCATCATATTCATCGACGAGATCGACTCCATTGCTCCCA
ACAGGGAGAAGACTCACGGCGAGGTGGAGAGGCGTATCGTTTCCCAGCTGCTGACGCTGATGGACGGCATGAAGGCCCGC
GCGCACGTCATCGTCATGGGCGCCACGAACCGTCCCAACAGCATCGACCCTGCCTTGAGGCGCTTCGGGAGGTTCGATCG
CGAGATCGACATCGGCGTGCCGGACGAGGTCGGGCGTCTCGAAGTGCTCCGCATCCACACCAAGAACATGAAGCTGGACG
AGGAGGTCAACCTTGAGGTGATTGCCAAGGATACGCACGGCTACGTCGGCGCCGACTTGGCCGCGCTCTGCACCGAGGCG
GCGCTGCAGTGCATCAGGGAGAAGATGGACGTGATC

Alignment

ORF - retro_hvul_59 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 66.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKSPNRLVVDEA-TNDDNSVVALHPDTMERLQLFRGDTVLLKGKKRKDTICIVLADDTCEEPKIRMNKTV
          KK..NRLVV..A.TNDDNSV..LHPDTME.L.LF.GDTVLLKGK.R..T.C..L.DDTCEE.K.R.NK..
Retrocopy KKAANRLVVEDASTNDDNSVCTLHPDTMEKLSLFKGDTVLLKGKRRHSTVCMALPDDTCEEHKMRINKVA

Parental  RKNLRVRLGDVVSVHQCPDVKYGKRVHILPIDDTVEGITGNLFDAFLKPYFLEAYRPLRKGDLFLVRGGM
          R.NLRVR..DVVSVH.C.DVKY..RVHILP.DDTVEGI.GNLFDA.LKPYF..A.RP..KGDLFLVRGGM
Retrocopy RSNLRVRIADVVSVHLCHDVKYARRVHILPLDDTVEGIAGNLFDAYLKPYFVDAFRPVHKGDLFLVRGGM

Parental  RSVEFKVIETDPA-EYCIVAPDTEIFCDGEPVKREDEERLDDVGYDDVGGVRKQMAQIRELVELPLRHPQ
          RSVEFKV.E.DPA..YCIV.PDTEIFC.GEPVKREDEERLDDVGYDDVGG..K...QIRELVELPLRHPQ
Retrocopy RSVEFKVMEIDPAADYCIVMPDTEIFCEGEPVKREDEERLDDVGYDDVGGMGKPLTQIRELVELPLRHPQ

Parental  LFKSIGVKPPKGILLFGPPGSGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAP
          .FKSIGVKPPKGILL.GPPGSGKTLIARAVANETGAFFFLINGPEIMSK.AGESESNLRKAFEEAEKNAP
Retrocopy IFKSIGVKPPKGILLYGPPGSGKTLIARAVANETGAFFFLINGPEIMSKMAGESESNLRKAFEEAEKNAP

Parental  SIIFIDEIDSIAPKREKTNGEVERRIVSQLLTLMDGLKSRAHVIVMGATNRPNSIDPALRRFGRFDREID
          SIIFIDEIDSIAP.REKT.GEVERRIVSQLLTLMDG.K.RAHVIVMGATNRPNSIDPALRRFGRFDREID
Retrocopy SIIFIDEIDSIAPNREKTHGEVERRIVSQLLTLMDGMKARAHVIVMGATNRPNSIDPALRRFGRFDREID

Parental  IGVPDEVGRLEVLRIHTKNMKLAEDVELEHISRDTHGYVGADLAALCTEAALQCIREKMDII
          IGVPDEVGRLEVLRIHTKNMKL.E.V.LE.I..DTHGYVGADLAALCTEAALQCIREKMD.I
Retrocopy IGVPDEVGRLEVLRIHTKNMKLDEEVNLEVIAKDTHGYVGADLAALCTEAALQCIREKMDVI

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_59 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G74922	1 retrocopy	retro_bdis_9,
Leersia perrieri	LPERR03G03650	1 retrocopy	retro_lper_1,
Hordeum vulgare	MLOC_74069	2 retrocopies	retro_hvul_38, retro_hvul_40,
Hordeum vulgare	MLOC_76416	1 retrocopy	retro_hvul_59 ,
Oryza glaberrima	ORGLA06G0255900	1 retrocopy	retro_ogla_73,
Populus trichocarpa	POPTR_0006s12740	1 retrocopy	retro_ptri_3,
Sorghum bicolor	Sb01g020910	1 retrocopy	retro_sbic_10,