RetrogeneDB ID: retro_hvul_88

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 6:518199153..518201355(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_9844
• Aliases: None
• Description: None

Sequence

>retro_hvul_88
CTGGAGGACGTGAAGAACGAGACGGTGGACCTGGAGACCATCCCGGTGCCGGAGGTCTTCAGCCACCTCAAGTGCAGCAA
GCAGGGGCTGAGCGGCACCGAGGCGCAGAACCGGCTCGCCATCTTCGGGCCCAACAAGCTGGAGGAGAAGACGGAGAACA
AGCTGCTCAAGTTCCTCGGCTTCATGTGGAACCCGCTGTCCTGGGTCATGGAGGCCGCCGCCATCATGGCCATCGTGCTC
GCCAACGGCGGCGGCAAGCCCCCCGACTGGCAGGACTTCGTCGGCATCGTCACCCTGCTCTTCATCAACTCCACCATCAG
CTTCATCGAGGAGAACAACGCCGGCAACGCCGCTGCCGCCCTCATGGCCGGCCTCGCCCCCAAAACCAAGTGTCTGAGGG
ACGGCAAGTGGAGCGAGATGGACGCCTCCTTCCTCGTACCCGGCGACATTATCAGCATCAAGCTCGGGGACATCATCCCC
GCCGACGCCAGGCTGCTCGAGGGCGACCCGCTCAAGGTCGACCAGGCCGCGCTCACCGGCGAGTCCATGCCCGTGAACAA
GCACTCCGGCCAGGGGGTTTTCTCCGGGTCGACGGTGAAGCAGGGCGAGATCGAGGCCGTCGTCATCGCCACCGGCGTGC
ACACCTTCTTCGGCAAGGCGGCGCACCTCGTCGACAGCACCAACAACGTCGGTCACTTCCAGCAGGTGCTCACCGCCATC
GGCAACTTCTGCATCATCTCCATCGCCGCCGGGATGCTGGTGGAGGTTGTCGTCATGTACCCGATCCAGCACCGCGCCTA
CCGCGACGGCATCGACAACCTGCTCGTGCTCCTCATCGGCGGCATCCCCATCGCCATGCCCACCGTGCTCTCCGTCACCA
TGGCCATCGGCTCCCACCGGCTGTCCCAGCAGGGCGCCATCACCAAGCGCATGACCGCCATCGAGGAGATGGCCGGCATG
GACGTGCTGTGCAGCGACAAGACGGGCACGCTCACGCTCAACAAGCTCACCGTCGACAAGACGCTCATCGAGGTGTACGG
CAGAGGGATAGACAAGGACACGGTGCTCCTCTACGCCGCCAGGGCGTCCCGCGTGGAGAACCAGGACGCCATCGACACAT
GCATCGTCGGCATGCTGGCCGACCCCAAGGAGGCCCGCGCCGGCATCCAGGAGGTGCACTTCCTCCCCTTCAACCCCGTG
GAGAAGCGCACGGCCATCACCTACATCGACGGCAACGGCGACTGGCACCGGATCAGCAAGGGCGCGCCGGAGCAGATCAT
CGAGCTGTGCAGGATGCCCAAGGAGGCCGAGAAGAGGGTCCACGGCCTGATCGACCAGTACGCCGACCGGGGGCTGCGGT
CGCTGGGCGTGTCGTACCAGCCGGTGCCGGCCAAGAACAAGGACAGCCCCGGCGAGCCGTGGCAGTTCGTGGGGCTGCTG
CCGCTGTTCGACCCGCCCCGGCACGACAGCGCGGAGACGATCCGGCGCGCGCTGCACCTGGGCGTGAACGTGAAGATGAT
CACCGGCGACCAGCTGGCCATCGGCAAGGAGACGGCGCGGCGGCTGGGCATGGGCACCAACATGTACCCTTCCACGACGC
TGCTGGGCGACAAGAGCACGGAGATGAGCGGGCTCCCCATCGACGAGCTGATCGAGAAGGCGGACGGGTTCGCCGGGGTG
TTCCCGGAGCACAAGTACGAGATCGTGAAGCGGCTGCAGGACCGGAAGCACATCTGCGGCATGACCGGGGACGGCGTGAA
CGACGCGCCGGCGCTGAAGAAGGCGGACATCGGGATCGCGGTGGACGACGCGACGGACGCGGCGCGGTCGGCGTCGGACA
TCGTGCTGACGGAGCCCGGGCTGAGCGTGATCGTGAGCGCGGTGCTCACCAGCCGCGCAATCTTCCAGCGGATGAAGAAC
TACACCATCTACGCCGTGTCCATCACCATCCGGATCGTGGTCGGGTTCATGCTGGTGGCGCTGCTGTGGAAGTTCGACTT
TGCGCCCTTCATGGTGCTCATCATCGCCATCCTCAACGACGGCACCATCATGACCATCTCCAAGGACCGCGTCAAGCCGT
CGCCCACCCCCGACTCGTGGAAGCTCAAGGAGATCTTCGCCACCGGCGTCGTCCTCGGCACCTACATGGCCCTCGTCACC
GTGCTCTTCTTCTACCTCGCCCACGACACCGAGTTCTTCCCG

Alignment

ORF - retro_hvul_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 76.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEAVLKEVVDLENIPLEEVLDNLRCSREGLTAEQAQQRLQIFGPNKLEEKEESKFLKFLGFMWNPLSWVM
          LE.V..E.VDLE.IP..EV...L.CS..GL....AQ.RL.IFGPNKLEEK.E.K.LKFLGFMWNPLSWVM
Retrocopy LEDVKNETVDLETIPVPEVFSHLKCSKQGLSGTEAQNRLAIFGPNKLEEKTENKLLKFLGFMWNPLSWVM

Parental  EAAAIMAIALANGGGKPPDWQDFVGIITLLVINSTISFIEENNAGNAAAALMARLAPKAKILRDGRWAEE
          EAAAIMAI.LANGGGKPPDWQDFVGI.TLL.INSTISFIEENNAGNAAAALMA.LAPK.K.LRDG.W.E.
Retrocopy EAAAIMAIVLANGGGKPPDWQDFVGIVTLLFINSTISFIEENNAGNAAAALMAGLAPKTKCLRDGKWSEM

Parental  DAAILVPGDVISIKLGDIIPADARLLEGDPLKIDQSALTGESLPATKGPGDGIYSGSTVKQGEIEAVVIA
          DA..LVPGD.ISIKLGDIIPADARLLEGDPLK.DQ.ALTGES.P..K..G.G..SGSTVKQGEIEAVVIA
Retrocopy DASFLVPGDIISIKLGDIIPADARLLEGDPLKVDQAALTGESMPVNKHSGQGVFSGSTVKQGEIEAVVIA

Parental  TGVHTFFGKAAHLVDSTNQVGHFQKVLTAIGNFCICSIAVGMFIEIIVMYPIQHRAYRPGIDNLLVLLIG
          TGVHTFFGKAAHLVDSTN.VGHFQ.VLTAIGNFCI.SIA.GM..E..VMYPIQHRAYR.GIDNLLVLLIG
Retrocopy TGVHTFFGKAAHLVDSTNNVGHFQQVLTAIGNFCIISIAAGMLVEVVVMYPIQHRAYRDGIDNLLVLLIG

Parental  GIPIAMPTVLSVTMAIGSHRLSQQGAITKRMTAIEEMAGMDVLCSDKTGTLTLNKLTVDKSLVEVFERGI
          GIPIAMPTVLSVTMAIGSHRLSQQGAITKRMTAIEEMAGMDVLCSDKTGTLTLNKLTVDK.L.EV..RGI
Retrocopy GIPIAMPTVLSVTMAIGSHRLSQQGAITKRMTAIEEMAGMDVLCSDKTGTLTLNKLTVDKTLIEVYGRGI

Parental  TQDQVILMAARASRTENQDAIDTAIVGMLADPKEARAGIQEVHFLPFNPTDKRTALTYIDADGKMHRVSK
          ..D.V.L.AARASR.ENQDAIDT.IVGMLADPKEARAGIQEVHFLPFNP..KRTA.TYID..G..HR.SK
Retrocopy DKDTVLLYAARASRVENQDAIDTCIVGMLADPKEARAGIQEVHFLPFNPVEKRTAITYIDGNGDWHRISK

Parental  GAPEQILHLAHNTSEIERRVHAVIDKFAERGLRSLAVAYQEVPDGRKESPGGPWHFAGLMPLFDPPRHDS
          GAPEQI..L.....E.E.RVH..ID..A.RGLRSL.V.YQ.VP...K.SPG.PW.F.GL.PLFDPPRHDS
Retrocopy GAPEQIIELCRMPKEAEKRVHGLIDQYADRGLRSLGVSYQPVPAKNKDSPGEPWQFVGLLPLFDPPRHDS

Parental  AETIRRALNLGVNVKMITGDQLAIGKETGRRLGMGTNMYPSSALLGQKNSDESISALPVDDLIEKADGFA
          AETIRRAL.LGVNVKMITGDQLAIGKET.RRLGMGTNMYPS..LLG.K......S.LP.D.LIEKADGFA
Retrocopy AETIRRALHLGVNVKMITGDQLAIGKETARRLGMGTNMYPSTTLLGDKSTE--MSGLPIDELIEKADGFA

Parental  GVFPEHKYEIVKRLQARKHICGMTGDGVNDAPALKKADIGIAVADATDAARSASDIVLTEPGLSVIISAV
          GVFPEHKYEIVKRLQ.RKHICGMTGDGVNDAPALKKADIGIAV.DATDAARSASDIVLTEPGLSVI.SAV
Retrocopy GVFPEHKYEIVKRLQDRKHICGMTGDGVNDAPALKKADIGIAVDDATDAARSASDIVLTEPGLSVIVSAV

Parental  LTSRAIFQRMKNYTIYAVSITIRIVLGFMLLALIWNFDFPPFMVLIIAILNDGTIMTISKDRVKPSPLPD
          LTSRAIFQRMKNYTIYAVSITIRIV.GFML.AL.W.FDF.PFMVLIIAILNDGTIMTISKDRVKPSP.PD
Retrocopy LTSRAIFQRMKNYTIYAVSITIRIVVGFMLVALLWKFDFAPFMVLIIAILNDGTIMTISKDRVKPSPTPD

Parental  SWKLAEIFTTGVILGGYLAIMTVIFFWAAYKTNFFP
          SWKL.EIF.TGV.LG.Y.A..TV.FF..A..T.FFP
Retrocopy SWKLKEIFATGVVLGTYMALVTVLFFYLAHDTEFFP

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_88 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_9844	1 retrocopy	retro_hvul_88 ,