RetrogeneDB ID: retro_hvul_15

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:438791530..438793471(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_62643
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_11567
• Aliases: None
• Description: None

Sequence

>retro_hvul_15
ATGGACGGATGGATGTTGCATGCAGACCAGATCGTGTGGATTACAGTGGCCATCCTGGTGGCCCTCTTCTCGGTGCAGCG
GTTCGGAACAGACAAGGTGGGCTACTTCTTCGCGCCGGTGGTCATCCTCTGGCTGCTCCTCATCGGCGGCGTCGGCGTGT
ACAACCTCGTGAAGCACGACATCGGCGTCCTCCGGGCCTTCAACCCCAAGTACATCGCCGACTACTTCCGGCGCAACAAG
AAGGACGCGTGGATCTCCCTCGGCGGCATCCTCCTCTGCTTCACCGGCACCGAGGCTCTCTTCGCCGACCTTGGCTACTT
CAGCATCCGCTCCATCCAGCTCAGCTTCGGCTTCGGCCTCGTCCCTTCTGTGCTCCTCGCCTACGCCGGCCAGGCCGCCT
TCCTCCGCAAGTACCCGGAGGAGGTGGCCAACACGTTCTACAGGTCCACCCCGACGGTCCTCTTCTGGCCCACCTTCGTC
CTCGCCATCGCCGCCTCCATCATCGGCAGCCAGGCCATGATCTCCTGCGCCTTCGCCACCATCTCCCACTCGCAGGCGCT
GGGATGCTTCCCGCGCGTCAAGATCCTGCACACCTCCAAGCAGTACCAGGGCCAGCTCTACATCCCGGAGGTCAACTTCC
TGCTGGGCTTCGCCGCTTGCGTCGTCACCGTGGCGTTCAAGACCACTGTGGTCATCGGCGAGGCGCACGGCATCTGTGTC
GTCCTCGTCATGCTCATCACCACGCTGCTCCTCACCGTGGTGATGCTTCTGGTGTGGAGGATGAACGCGTGGTGCGTGGC
GCTCTTCTTCTTGGTCTTCATGGCGTCCGAGTCCGTCTACCTCTCCTCGGTGCTCTACAAGTTCCTGCACGGAGGGTACA
TCCCCGTGGTCATCTCGGCGGTGCTCATGGCCGTCATGATCGTGTGGCACTACGTGCACGTGATGCGCTACAAGTACGAG
CTGGAGCGCACGGTGTCGCCGGACAAGGTGCGGGAGATGCTGGACGGCCGCGACCTGCGCAAGGTGCCCGGCGTGGGGCT
CTTCTACACGGACCTCGTGCAGGGGATCCCGCCGGTGTTCCCGCACCTGATCGAGAAGATCCCGTCCATCCACGCCGTGC
TCCTCTTCGTGTCCGTGAAGCACCTCCCCGTCCCGCACGTGGACATGTCGGAGCGGTTCCTGTTCCGGCAGGTGGAGCCG
AGGGAGCACAAGCTGTACCGGTGCGTGGCGAGGTACGGGTACCGTGACCCGCTGGAGGAGGCCAAGGACTTCGCGACCAA
CCTGGTGGAGCGCCTCCAGTACTACATCCGCGACGTGAACCTGTACGGCGTGGACGTGGACGCCAAGGCCGGCAAGGTGA
GCTACCCGAGCTCGCGCTGCGACAGCATGGCCAGATCAACCCGGCGCAGCAGCATGACGATGACGATGCAGCAGCACTAC
TCGTCGGCGTCCTACACGGAGAGCCTTGCGCTGGCGAGGGCAAGGTCGACGTCGTCGGGGGCCACCGGGCGCATGAACAT
GAACGGCATGATCATGATGCCGTCGGCGTCCTACACGGAGAGGGAGAGGCAGGGGCGGTCCATCTACGCGGAGGAGATGA
TGACGCCGGCCGAGTCCTTCTCGGAGCTGGCAATGCAGGTGGTGCCGTCGGGGCGGTACGCGGCGAGCAGCCAGCAGCTT
TTCCAGGCGGCCAAGATGAGCCTGGAGGAGATGGCCAAGATCGAGGAGGAGCAGAGGTACATCGAGAGGGAGATGGAGAA
GGGGGTGGTGTACATCATGGGGGAGAACGAGGTGGTGGCGCGGCCTCACTCCTCGCTGCTCAAGAAAATCATCGTCAATT
ATGTATACGCCTTCCTGAGGAAGAACTGCAGGCAAGGGGATAAGATGCTCGCCATCCCAAGAAGCCAACTGCTCAAGGTC
GGAATGTCTTACGAGATCTAG

Alignment

ORF - retro_hvul_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.0 %
• Parental protein coverage: 56.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTTDQIVWITVGILILFFAVQHLGTDKIGYTFAPLVVVWLLLIAGIGLYNLIKYDIGTLRAFNPKYIFDY
          L..DQIVWITV.IL...F.VQ..GTDK.GY.FAP.V..WLLLI.G.G.YNL.K.DIG.LRAFNPKYI.DY
Retrocopy LHADQIVWITVAILVALFSVQRFGTDKVGYFFAPVVILWLLLIGGVGVYNLVKHDIGVLRAFNPKYIADY

Parental  FRRNKKKGWVSLGEILLCFTGTEALFADLGYFSIKSIQLSFSFGLLPSVLLTYIGQAAYLRKHLDMQISN
          FRRNKK..W.SLG.ILLCFTGTEALFADLGYFSI.SIQLSF.FGL.PSVLL.Y.GQAA.LRK.......N
Retrocopy FRRNKKDAWISLGGILLCFTGTEALFADLGYFSIRSIQLSFGFGLVPSVLLAYAGQAAFLRKYPE-EVAN

Parental  AFFNSIPSTLFWPTFVLALLASVIGSQAMVSCAFATMSHLQTLSCFPRVKILHTSRRYSGQLYIPEVNFF
          .F..S.P..LFWPTFVLA..AS.IGSQAM.SCAFAT.SH.Q.L.CFPRVKILHTS..Y.GQLYIPEVNF.
Retrocopy TFYRSTPTVLFWPTFVLAIAASIIGSQAMISCAFATISHSQALGCFPRVKILHTSKQYQGQLYIPEVNFL

Parental  LCVASCIVTLSFRTTGFIAKAHEICVALVMVITTLLMTIVMLLVWKVNIWWIAAFFAVFMSTETVYLSAV
          L..A.C.VT..F.TT..I..AH.ICV.LVM.ITTLL.T.VMLLVW..N.W..A.FF.VFM..E.VYLS.V
Retrocopy LGFAACVVTVAFKTTVVIGEAHGICVVLVMLITTLLLTVVMLLVWRMNAWCVALFFLVFMASESVYLSSV

Parental  LYKFTQGPYFPLAMSAVLMVIMIVWHYVHVKRYKYELQHTVSPDEVRHLLERHDLKRVPGLGLFYTELVQ
          LYKF..G.Y.P...SAVLM..MIVWHYVHV.RYKYEL..TVSPD.VR..L...DL..VPG.GLFYT.LVQ
Retrocopy LYKFLHGGYIPVVISAVLMAVMIVWHYVHVMRYKYELERTVSPDKVREMLDGRDLRKVPGVGLFYTDLVQ

Parental  GIPPIFPHLIEKIPTVHSVIVFISVKHLPIPHVDVQERFLFRQVEPKESMVFRCVARYGYRDTLEMAGDF
          GIPP.FPHLIEKIP..H.V..F.SVKHLP.PHVD..ERFLFRQVEP.E....RCVARYGYRD.LE.A.DF
Retrocopy GIPPVFPHLIEKIPSIHAVLLFVSVKHLPVPHVDMSERFLFRQVEPREHKLYRCVARYGYRDPLEEAKDF

Parental  VATLVEYLQYYVRDLSLY---CTAEPLRTSYPSIRIDS
          ...LVE.LQYY.RD..LY.....A.....SYPS.R.DS
Retrocopy ATNLVERLQYYIRDVNLYGVDVDAKAGKVSYPSSRCDS

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_15 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_11567	1 retrocopy	retro_hvul_15 ,