RetrogeneDB ID: retro_hvul_80

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:350115270..350116749(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_55525
• Aliases: None
• Description: None

Sequence

>retro_hvul_80
ACCCTGTTCGTGTTCATGGCGTGCCTGGTTGCAGCGACGGGCGGGCTGATCTTCGGCTACGACATCGGCATCTCCGGCGG
GGTGACGTCCATGGACCCCTTCCTCAGCAAGTTCTTCCCGTCGGTCTACCGCAAGCAGGCCGAGGCCGCCGACGACAACC
AGTACTGCAAGTTCGACAGCCAGATCCTCACCATGTTCACCTCCTCGCTCTACCTCGCCGCGCTCGTCGCCTCCCTCTTC
GCCGCCTCCGTCACCCGCGTCGCCGGGCGCAAGTGGTCCATGTTCGTCGGCGGGATCACCTTCCTCGTCGGCTGCGCGCT
CAACGGCGCCGCCGAGAACATGGCCATGCTCATCCTCGGCCGCGTCTTCTTGGGTGTCGGCGTCGGCTTCGCCAACCAGA
GCGTGCCGGTGTACCTGTCCGAGATGGCGCCCGCGAAGATGCGCGGCATGCTCAACAACGGCTTCCAGCTCATGATCACG
CTCGGCATCCTCGCCGCCAACCTCATCAACTACGGCACAGCCAAGATCGCCGCCGGGTGGGGCTGGAGGCTCAGCCTCGC
GCTCGCGGCCGTCCCTGCGGCCATCATCACCATCGGGTCGCTGTTCCTCCCGGACACGCCCAACTCCCTCCTGGAACGCG
GCAAGGCCGACGACGCCAGGCGGATGCTCCAGCGCGTGCGCGGCATCCAATACGTCGACGAAGAGTACCACGACCTGGCG
GCGGCGAGCGAGGCGTCCAGCGCCATCAAGCGCCCGTGGCGGGACATCCTGCGGCGGAGGTACAGGCCGCAGCTCGTGAT
GGCGGTGGCGATCCCGCTGCTGCAGCAGCTCACGGGCATCAACGTGATCATGTTCTACGCGCCGGTGCTGTTCAAGACGC
TCGGCTTCGGCGGCAGCGCGTCGCTCATGTCGGCGGTCATCACCGGCGGGGTCAACCTGGCGGCGACGCTGGTGTCAATC
TTCACCGTCGATAGGGTGGGCAGGCGTGCGCTGCTCCTGCAGGGAGGGGCGCAGATGTTCGTGAGCCAGGTGGCAGTGGG
GGCGCTCATCGGCGCCAAGCTCGGGTGGAGCGGGGTGGCGGAGATCCCGGCGGGGTACGCGGCGGCGGTGGTGGTGGTGA
TGTGCGTCTACGTGGCGGGGTTCGCGTGGTCGTGGGGCCCGCTGGGGTGGCTGGTGCCGAGCGAGGTGATGCCGCTGGAG
GTGCGGCCGGCGGGGCAGAGCATCACCGTGGCAGTCAACATGCTCATGACCTTCGTCGTCGCGCAGGCCTTCCTCCCCAT
GCTCTGCCGCCTCAAGTTCGTCCTCTTCTTCTTCTTCGCTGCCTGGGTCGCCGCCATGACGCTCTTCGTCGCGCTCTTCG
TGCCGGAGACAAAGGGGGTGCCCATCGAGGACATGGCCAACGTGTGGAAGGCGCACTGGTACTGGAAGCGTTTCGTCACC
GACGACGGCGATGCCCCCCGACGTGCGGACGTCGAGATG

Alignment

ORF - retro_hvul_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.95 %
• Parental protein coverage: 93.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TMFVLFACIVAATGGLIFGYDIGISGGVTSMNPFLMKFFPGVYHKEQEAERNQSNQYCKFDSQLLTMFTS
          T.FV..AC.VAATGGLIFGYDIGISGGVTSM.PFL.KFFP.VY.K..EA.....NQYCKFDSQ.LTMFTS
Retrocopy TLFVFMACLVAATGGLIFGYDIGISGGVTSMDPFLSKFFPSVYRKQAEAA--DDNQYCKFDSQILTMFTS

Parental  SLYLAALVASFFAATVSRVAGRKWSMFAGGVTFLVGAALNGAAKNVLMLILGRVLLGIGVGFANQSVPVY
          SLYLAALVAS.FAA.V.RVAGRKWSMF.GG.TFLVG.ALNGAA.N..MLILGRV.LG.GVGFANQSVPVY
Retrocopy SLYLAALVASLFAASVTRVAGRKWSMFVGGITFLVGCALNGAAENMAMLILGRVFLGVGVGFANQSVPVY

Parental  LSEMAPARLRGMLNIGFQLMVTIGILCANLINYGTSKIKGGWGWRVSLALAAVPAGIIAIGALFLPDTPN
          LSEMAPA..RGMLN.GFQLM.T.GIL.ANLINYGT.KI..GWGWR.SLALAAVPA.II.IG.LFLPDTPN
Retrocopy LSEMAPAKMRGMLNNGFQLMITLGILAANLINYGTAKIAAGWGWRLSLALAAVPAAIITIGSLFLPDTPN

Parental  SLIDRGYTDDAKKMLRRVRGTDDVEEEYSDLVAASDESKLVSHPWRNILQRRYRPQLTFAIAIPFFQQLT
          SL..RG..DDA..ML.RVRG...V.EEY.DL.AAS..S.....PWR.IL.RRYRPQL..A.AIP..QQLT
Retrocopy SLLERGKADDARRMLQRVRGIQYVDEEYHDLAAASEASSAIKRPWRDILRRRYRPQLVMAVAIPLLQQLT

Parental  GINVIMFYAPVLFKTLGFADDASLMSAVITGLVNVFATFVSIVTVDRLGRRKLFLQGGTQMLACQIVVGS
          GINVIMFYAPVLFKTLGF...ASLMSAVITG.VN..AT.VSI.TVDR.GRR.L.LQGG.QM...Q..VG.
Retrocopy GINVIMFYAPVLFKTLGFGGSASLMSAVITGGVNLAATLVSIFTVDRVGRRALLLQGGAQMFVSQVAVGA

Parental  LIGAKFGFTGVADIPRGYAAFVVFFICAYVAGFAWSWGPLGWLVPSEIFPLEIRSAGQSITVSMNMLCTF
          LIGAK.G..GVA.IP.GYAA.VV...C.YVAGFAWSWGPLGWLVPSE..PLE.R.AGQSITV..NML.TF
Retrocopy LIGAKLGWSGVAEIPAGYAAAVVVVMCVYVAGFAWSWGPLGWLVPSEVMPLEVRPAGQSITVAVNMLMTF

Parental  IIAQAFLPMLCRFKFMLFFFFGAWVIVMTLFVAFFLPETKNVPIEEMVLVWKAHWYWGRFIRDE-DVHVG
          ..AQAFLPMLCR.KF.LFFFF.AWV..MTLFVA.F.PETK.VPIE.M..VWKAHWYW.RF..D..D....
Retrocopy VVAQAFLPMLCRLKFVLFFFFAAWVAAMTLFVALFVPETKGVPIEDMANVWKAHWYWKRFVTDDGDAPRR

Parental  ADVEM
          ADVEM
Retrocopy ADVEM

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_80 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 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,