RetrogeneDB ID: retro_hvul_3

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 2:606967305..606968661(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_80496
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_2703
• Aliases: None
• Description: None

Sequence

>retro_hvul_3
ATGCAAAACATATCGGCACCAGCAGTTGAGCAAACCCAGCAAAGCTCACTCACTCTAGTGATCACTTTCACTTGGCAACC
CAGGAAGCGATCGAGGGAAGCAGCCATGATGCTTCGCATGCAAAGCCTCTGCCCTCCTCGTCGTGTGTCGGTGGACGGCC
CGATCATCGTCGGCGCCGGCCCCTCCGGGCTCGCCGTGGCGGCCAGCCTCGGCGAGGAGGGCATGCCGTTCCTCATGCTG
GAGCGCGAGGACTGCATCGCCTCGCTCTGGCAGAAGCGCACCTACGACCGCGTCAAGCTCCACCTCCCCAAGCACTTCTG
CGAGCTCCCTCGCATGCCCTTCCCGGACAGCTACCCGGAGTACCCCACCCGCCGCCAGTTCATCGACTACCTCGAGACCT
ACGCCGCCAGGTTCGACATCAAGCCGGAGTTCAACACCACCGTGCTCTCCGCCCACTACGACAACACCTCCGGGCTCTGG
CACGCGCAGGCCACCCGCGCGGGCGGCGCCCAGGTGGAGTACATCGGCCGCTGGCTCGTGGTCGCCACCGGCGAGAACGC
CGTCAACGTCGTCCCGGACATCCCGGGCCTCGGCGGCTTCTGCGGCGAGGTCACCCACGTCAGCCACTACAAGTCCGGCG
AGCCCTACAACGGGAAGCGCGTGCTCGTCGTCGGCTGCGGGAACTCCGGCATGGAGGTCTCCCTCGACCTCTGCGACCAC
GGCGCCCACCCTTTCATGGTGGTGCGCGACGCCATGCACGTCATTCCGCGCGAGGTGCTCGGCAAGTCCACCTTCGAGCT
CGCCATGCTGCTCATGGCGTGGCTCCCGCTCTGGTTCGTGGACAAGATCATGATCTTCCTCGCCTGGCTCGTCCTCGGCG
ACCTCGACAAGCTCGGCATCCACCGCCCGGCTGTCGGCCCGCTCACGCTCAAGCACACGCAGGGACGGGCCCCGGTGCTC
GACACCGGCGCGCTCGCCAGGATTAGGAGTGGCCAAATCACCGTCGTCCCCGGCATCACCCGCTTCACGAACTCCGACGC
CGTGCTGTCCGATGGCACCGCCGTCCATGTCGATGCTGTCATCCTCGCCACCGGATACAGAAGCAATGTGCCACAGTGGC
TCCGGGCAACGGACTTCTTCGGCAAGGACGGCTACCCGAAGACGGAGTTCCCCAACGGCTGGAAGGGCCAGTTTGGCCTC
TACTCCGTCGGCTTCGCACGCCGCGGCATCTCCGGTGCCTCCGCCGATGCCGTGCGCATCGCCAAGGACCTCTGCCAGCT
CTGGAAGGAGGAGACCACGCCCACAAAGAAGGCCGGCCGGCCATCCTACAGGAGGTCTATCTCCGTCGTCTTGTAA

Alignment

ORF - retro_hvul_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.26 %
• Parental protein coverage: 86.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPGPIIVGAGPSGLAVAACLKEKGVDSLILERSNCIASLWQLKTYDRLSLHLPRQFCELPLMPFPADYPI
          V.GPIIVGAGPSGLAVAA.L.E.G...L.LER..CIASLWQ..TYDR..LHLP..FCELP.MPFP..YP.
Retrocopy VDGPIIVGAGPSGLAVAASLGEEGMPFLMLEREDCIASLWQKRTYDRVKLHLPKHFCELPRMPFPDSYPE

Parental  YPSKEKFVAYLEKYAARFGICPRYNHAVVRAEYDEKLLLWRVRSQLTGRMEEEVEYLSRWLVVATGENAE
          YP....F..YLE.YAARF.I.P..N..V..A.YD....LW.......G.....VEY..RWLVVATGENA.
Retrocopy YPTRRQFIDYLETYAARFDIKPEFNTTVLSAHYDNTSGLWHAQATRAGGAQ--VEYIGRWLVVATGENAV

Parental  VVQPEIDGLKEFKGTVVHTSAYKTGSAFAGKRVLVVGCGNSGMEVCLDLCDHNAQPHIVVRDTVHILPRE
          .V.P.I.GL..F.G.V.H.S.YK.G....GKRVLVVGCGNSGMEV.LDLCDH.A.P..VVRD..H..PRE
Retrocopy NVVPDIPGLGGFCGEVTHVSHYKSGEPYNGKRVLVVGCGNSGMEVSLDLCDHGAHPFMVVRDAMHVIPRE

Parental  MLGQSTFGLSMWLLKWFPVHVVDRILLLVARTMLGDTARLGLKRPTVGPLELKSLSGKTPVLDVGTFAKI
          .LG.STF.L.M.L..W.P...VD.I....A...LGD...LG..RP.VGPL.LK...G..PVLD.G..A.I
Retrocopy VLGKSTFELAMLLMAWLPLWFVDKIMIFLAWLVLGDLDKLGIHRPAVGPLTLKHTQGRAPVLDTGALARI

Parental  RSGDIKVLPGIKKISGRQVEFLDTRSEDFDAIVLATGYKSNVPFWLKDRELFSDKDGLPRKAFPNGWKGE
          RSG.I.V.PGI...........D......DA..LATGY.SNVP.WL.....F..KDG.P...FPNGWKG.
Retrocopy RSGQITVVPGITRFTNSDAVLSDGTAVHVDAVILATGYRSNVPQWLRATDFFG-KDGYPKTEFPNGWKGQ

Parental  RGLYSVGLTRRGLMGTSVDARRIAHDIEQ
          .GLYSVG..RRG..G.S.DA.RIA.D..Q
Retrocopy FGLYSVGFARRGISGASADAVRIAKDLCQ

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_3 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_2703	1 retrocopy	retro_hvul_3 ,