RetrogeneDB ID: retro_hvul_21

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 6:308488340..308489942(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_15141
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_58639
• Aliases: None
• Description: None

Sequence

>retro_hvul_21
ATGGCAAGAAGTTGCCTCGCTGCGTTTCTTCTCTGCATGGCCAGCTTCCTCTCCGCCGTCGCCGGCCAACTCCGGCCAAT
GCCTGCGGGTGGCCTTCCCAGTGATCTCGTTGCCCTAGGAATGGCCTCGAAGATCCAAACCGACCGCAACTCGACGGCGA
GGGCGTCATCAGACTTTGGCCGCATGGTGGAGGCGGCGCCGGAAGCCGTTCTACAGCCTGCCACGGCCGCCGACATCGCC
GAGCTCATCCGGTTTTCCACGTCGTCGCCGGTGCCATTCCCCGTGTCACCACGCGGGCAGGGCCATTCCGTCCGCGGGCA
GTCTCTCGCTCCAGGCGGCGTCGTGGTCGACATGCGCGCGCTGGGGCGTGGTGACCACCGCATCAACGTGTCTGCAGACT
ACGTCGACGCCGGCGGCGAGCAGCTGTGGGTCGACGTCCTCCGCGGGACGCTGACGCACGGTCTCGCGCCCTGTGCGTGG
ACGGACTACCTGCGGCTCACCGTCGGTGGCACACTTTCTAACGCCGGCATCGGCGGGCAAGCGTTCCGGCACGGCCCGCA
GATCGCCAACGTGCACGAGCTCGACGTGGTTACCGGGACGGGTGAGATGGTGACATGCTCACCTCACAAAAGGAAGGACC
TGTTCTTCGCGGTGTTAGGCGGGCTGGGCCAGTTTGGGATCATAACTCGGGCGCGGATCGCGCTTGAGCCGGCCCCAAAG
CAGGTGCGCTGGGTTCGACTCGCCTACTCAGACGTGGTTGCGTTCACCAGAGACCAGGAGCTGCTCATTTCCAAGCAGGC
TAGCGAAGCCGGGTTCGACTATGTGGAGGGCCAAGTCCAGCTTAATCGGACACTAACCGAGGGGCCCAAGTCGACGCCTT
TCTTCTCCGAAGCCGACATCAACAGGCTTGCTTCCCTCGCGTCGGAGACTGGCTCCAGGGCGATCTACTTCATCGAAGCC
GCAATGTACTACGATGAGACCACTGCCCCTTACGTCGATCAGAAACTAGAGACGGTGCTAGCTCAACTGAGCTTTGTACC
CGGGTTCGTGTTCACCAAGGATGTGACGTACTTGCAGTTCCTCGACCGCGTGCGCGTGGAGGAGGTTGTGCTTCGGTCTG
CTGGCGTGTGGGATGTGCCACACCCATGGCTGAACCTCTTCATCCCCCGTTCACGCATTCTCGACTTCGACGCTGGCGTG
CTCAAAGGCATCCTCGGGGGTGACAACCCAGTCGGGCTCATCCTCATGTACCCCATGAACACGGCCAAATGGAACTCCCA
GATGACGGCGGTAACGCCACCCACTCGCGAGGACGTATTCTACACCGTGGGACTTCTCCGGTCGGCTCTATCCACCAATG
AACTGGAGCGGCTACAGAGGGAGAACCAGTCGGTGCTAGCATTTTGCGACAAGGAGGGCATTGAGTGCAAGCAGTATCTG
CCACACTACACGTGTCAAGATGGATGGCGGCGACATTTTGGCCCCAAGTGGAGGAAAATCACACAACTCAAGGCCAAATA
TGACCCCCACGCCATAATGTCGCCAGGGCAGAGAATTTTTCAATTGCCAAGTGTGCCAACGACAAGCACTACAGCCGCAT
AA

Alignment

ORF - retro_hvul_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.83 %
• Parental protein coverage: 94.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLAALAAAGKLRSDPNATLAASTDFGNITAALPAAVLFPSSPADVAALLRAAHSTAAWPYTISFRGRGHS
          DL.AL..A.K...D.N.T..AS.DFG....A.P.AVL.P...AD.A.L.R...S....P...S.RG.GHS
Retrocopy DLVALGMASKIQTDRNSTARASSDFGRMVEAAPEAVLQPATAADIAELIRFSTSSPV-PFPVSPRGQGHS

Parental  VMGQALAPGGVVVDMPSLGGPSSAARINVSVDGQYVDAGGEQMWIDVLRATLERGVAPRSWTDYLHLTVG
          V.GQ.LAPGGVVVDM..LG......RINVS.D..YVDAGGEQ.W.DVLR.TL..G.AP..WTDYL.LTVG
Retrocopy VRGQSLAPGGVVVDMRALGRGDH--RINVSAD--YVDAGGEQLWVDVLRGTLTHGLAPCAWTDYLRLTVG

Parental  GTLSNAGISGQTYRHGPQISNVLELDVITGYGETVTCSKSLSPDLFDAVLGGLGQFGVIVRARIALEPAP
          GTLSNAGI.GQ..RHGPQI.NV.ELDV.TG.GE.VTCS.....DLF.AVLGGLGQFG.I.RARIALEPAP
Retrocopy GTLSNAGIGGQAFRHGPQIANVHELDVVTGTGEMVTCSPHKRKDLFFAVLGGLGQFGIITRARIALEPAP

Parental  ARARWARLVYTDFATFSADQERLVAPGPDGAFGPMGYIEGAVYVNHSLAAGLKNAGGFFTDADVARIVAV
          ...RW.RL.Y.D...F..DQE.L.......A.....Y.EG.V..N..L..G.K....FF..AD..R....
Retrocopy KQVRWVRLAYSDVVAFTRDQELLISKQASEA--GFDYVEGQVQLNRTLTEGPKST-PFFSEADINRLASL

Parental  AAARNATTVYVIEATLNYDNATAASVDQELKSVLATLKYEEGLAFVRDASYLEFLDRVHGEEVALEKLGL
          A........Y.IEA...YD..TA..VDQ.L..VLA.L....G..F..D..YL.FLDRV..EEV.L...G.
Retrocopy ASETGSRAIYFIEAAMYYDETTAPYVDQKLETVLAQLSFVPGFVFTKDVTYLQFLDRVRVEEVVLRSAGV

Parental  WRVPHPWLNVLVPRSGIADFDRGVFRGILQGTDIAGPLVVYPLNKSKGDDGMSAVTP--AEEVFYAVSML
          W.VPHPWLN...PRS.I.DFD.GV..GIL.G....G....YP.N..K....M.AVTP...E.VFY.V..L
Retrocopy WDVPHPWLNLFIPRSRILDFDAGVLKGILGGDNPVGLILMYPMNTAKWNSQMTAVTPPTREDVFYTVGLL

Parental  FSSVA-NDLRRLEAQNQKILRFCDLAGIGYKEYLAHYTAHGDWVRHFGGKWKHFVEMKDKYDPKKLLSPG
          .S....N.L.RL...NQ..L.FCD..GI..K.YL.HYT....W.RHFG.KW......K.KYDP....SPG
Retrocopy RSALSTNELERLQRENQSVLAFCDKEGIECKQYLPHYTCQDGWRRHFGPKWRKITQLKAKYDPHAIMSPG

Parental  QDIFKL
          Q.IF.L
Retrocopy QRIFQL

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_21 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_58639	1 retrocopy	retro_hvul_21 ,