RetrogeneDB ID: retro_hvul_35

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:517983131..517984736(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_69871
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_4708
• Aliases: None
• Description: None

Sequence

>retro_hvul_35
ATGACTGCCTCCGCCTCCGCGCGTAGGATGGCCTTCGCCGCGGCGGCCTCCCTGGCCGTGTACTGGCTCCTCAAGTCGTT
CCTCCACACACCTCACCCCGCGCTGCTGCCGGCGGCGGCGGCCCTCGTGGCCCTCACCATCACTCTGGGAGCTTCGGGGA
AGGGTGGCGGCGCCGGCGCTCCTCCCGGGCCCGCGGCCGTGCCGGTGTTCGGCAACTGGCTGCAGGTGGGCAACGACCTC
AACCACCGCTTCCTGGCAGGGCTTTCGGCGCGGTACGGCCCCGTGTTCCGCCTGCGGCTGGGCGTGCGCAACCTGGTGGT
GGTGTCGGACCCGCGGCTGGCCACGGAGGTGCTCCACACGCAGGGCGTGGAGTTCGGGTCCCGCCCGCGGAACGTCGTCT
TCGACATCTTCACGGCCAACGGCGCCGACATGGTCTTCACCGAGTACGGCGATCACTGGCGCCGCATGCGCCGCGTCATG
ACGCTGCCCTTCTTCACGGCGCGCGTCGTGCAGCAGTACCGCGCCATGTGGGAGGCCGAGATGGACGACGTCGTGTCCGA
CCTGCGCGGCGGCTCCGCCGCCCGCGGCCCCGGCGTCGTCGTTCGCCGCAGGCTGCAGCTCATGCTCTACAACATCATGT
ACCGCATGATGTTCGACGCCCGCTTCGAGTCCGTGGACGACCCCATGTTCGTGGAGGCCACCAAGTTCAACTCGGAGCGC
AGCCGCCTGGCGCAGAGCTTCGACTACAACTACGGCGACTTCATCCCCATCCTCAGGCCCTTCCTGCGTGGCTACCTCAA
CAAATGCAGGGACCTGCAGACCAGGAGGCTTGCCTTCTTCAACAGCAACTACGTCGAGAAGAGAAGGAAGGTGATGGACA
CGCCGGGGGACAAGAACAAGCTCCGATGCGCGATCGACCACATCCTCGCAGCGGAGAAGAGCGGCGAGATCACGCCGGAG
AACGTCATCTACATCGTCGAGAACATCAACGTCGCGGCCATCGAGACGACGCTATGGTCCATCGAGTGGGCGCTGGCCGA
GGTCGTGAACCACCCGGACGTGCAGCGCAAGGTCCGCGGCGAGATCAGGGACGTGCTCGGCGACGACGAGCCCATCACCG
AGTCCAACATCAGCAAGCTGCCGTACCTGCAGGCCGTGATCAAGGAGACGCTGCGGCTGCACTCCCCCATCCCGCTCCTC
GTCCCCCACATGAACCTCGAGGAGGCCAGCCTCGGCGGCTACACCATTCCCGAGGGCTCCAAGGTCGTCGTCAACGCCTG
GTGGCTGGCCAACAACCCGGAGCTGTGGGAGAAGCCGGAGGAGTTCAGGCCGGAGAGATTCTTGGGCGAGGAGAGCAACG
TGGACGCCACGGTCGGCGGCAAGGTGGACTTCCGGTTCCTCCCGTTCGGCGTGGGCCGGCGCAGCTGCCCCGGCATCATC
CTCGCGCTGCCCATCCTTGCGCTCATCGTCGGGAAGCTCGTGAGGAGCTTCGAGATGGTGCCCCCGCCAGGCGTGGACAA
GCTCGACGTGAGCGAGAAAGGCGGGCAGTTCAGCCTCCACATTGCCAACCATTCCCTCGTCGCATTCCACCCCATCTCAG
CATGA

Alignment

ORF - retro_hvul_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.89 %
• Parental protein coverage: 92.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPGPIPVPIFGNWLQVGDDLNHRNLAAMARKFGEVFLLRMGQRNLVVVSSPPLAREVLHTQGVEFGSRTR
          PPGP..VP.FGNWLQVG.DLNHR.LA......G.VF.LR.G.RNLVVVS.P.LA.EVLHTQGVEFGSR.R
Retrocopy PPGPAAVPVFGNWLQVGNDLNHRFLAGLSARYGPVFRLRLGVRNLVVVSDPRLATEVLHTQGVEFGSRPR

Parental  NVVFDIFTGEGQDMVFTVYGDHWRKMRRIMTVPFFTNKVVQQYRPGWEAEAAFVVDNVRADPRAATEGVV
          NVVFDIFT..G.DMVFT.YGDHWR.MRR.MT.PFFT..VVQQYR..WEAE...VV...R....A...GVV
Retrocopy NVVFDIFTANGADMVFTEYGDHWRRMRRVMTLPFFTARVVQQYRAMWEAEMDDVVSDLRGGSAARGPGVV

Parental  LRRHLQLMMYNNMYRIMFDRRFESMDDPLFLRLRALNGERSRLAQSFEYNYGDFIPILRPFLRGYLRLCK
          .RR.LQLM.YN.MYR.MFD.RFES.DDP.F......N.ERSRLAQSF.YNYGDFIPILRPFLRGYL..C.
Retrocopy VRRRLQLMLYNIMYRMMFDARFESVDDPMFVEATKFNSERSRLAQSFDYNYGDFIPILRPFLRGYLNKCR

Parental  EVKETRLKLFKDYFLDERKKLASTKAMDNNGLKCAIDHILEAEQKGEINEDNVLYIIENINVAAIETTLW
          .....RL..F.......R.K...T...D.N.L.CAIDHIL.AE..GEI...NV.YI.ENINVAAIETTLW
Retrocopy DLQTRRLAFFNSNYVEKRRKVMDTPG-DKNKLRCAIDHILAAEKSGEITPENVIYIVENINVAAIETTLW

Parental  SIEWGLAELVNHPEIQQKLRDEMDAVLGVGQQITEPDTHRLPYLQAVIKETLRLRMAIPLLVPHMNLHDA
          SIEW.LAE.VNHP..Q.K.R.E...VLG....ITE.....LPYLQAVIKETLRL...IPLLVPHMNL..A
Retrocopy SIEWALAEVVNHPDVQRKVRGEIRDVLGDDEPITESNISKLPYLQAVIKETLRLHSPIPLLVPHMNLEEA

Parental  KLAGYNIPAESKILVNAWFLANNPEQWKRPDEFRPERFLEEEKHVEANGN---DFRYLPFGVGRRSCPGI
          .L.GY.IP..SK..VNAW.LANNPE.W..P.EFRPERFL.EE..V.A......DFR.LPFGVGRRSCPGI
Retrocopy SLGGYTIPEGSKVVVNAWWLANNPELWEKPEEFRPERFLGEESNVDATVGGKVDFRFLPFGVGRRSCPGI

Parental  ILALPILGITIGRLVQNFVLTPPPGQDKLDTTEKGGQFSLHILKHSTIVAKP
          ILALPIL....G.LV..F...PPPG.DKLD..EKGGQFSLHI..HS.....P
Retrocopy ILALPILALIVGKLVRSFEMVPPPGVDKLDVSEKGGQFSLHIANHSLVAFHP

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_35 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G010468	1 retrocopy	retro_zmay_26,
Hordeum vulgare	MLOC_4708	1 retrocopy	retro_hvul_35 ,
Sorghum bicolor	Sb03g038160	1 retrocopy	retro_sbic_33,