RetrogeneDB ID: retro_hvul_91

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:60824135..60825092(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_36995
• Aliases: None
• Description: None

Sequence

>retro_hvul_91
ATCCCCACCGTGGACGTGGACCGCCTGGCCGACGCCGATGCCGGCGAGGCCGACAAGCTCCGGTCGGCGCTCGCCTCCTG
GGGCCTCTTCGCGGTGACCGGCCACGGCATGACGGATCCGTTCCTCGACGCGATCCTCGGCGCGGCGCGCGGGTTCTTCC
ACCTGCCGATGGAGGCCAAGCAGGAGTACCGCAACGTGGTGGACGCCGACGACGGCGGCCGCAAGTTCCAGCCCGAGGGC
TACGGCGTCGACCGCGTCGACACGGACGAGCAGGTCCTCGACTGGTGCGACCGGCTCTACCTCCAGGTCCGCCCGGACGA
CGCGCGGCAGCTCCGCTTCTGGCCGACTCACCCGTCGGACCTCGCCGAGCTCCTCAAAGAGTTCAGCGTCGAGGGCGAGA
AGGTGGCCAAGCTCGTCGTCACGGCCATGGCGAGGTGCCTGGGCTTCGAGGAGGGGTTCTTCTTGGACAAGGTCGGCGAG
CGGATGCCGTCCTACGCGCGCTTCACCTACTACCCGCCGTGCCCGCGCCCGGACCTCGTGCACGGGCTCAAGCCCCACAC
CGACAACTCCGTGGTCACCGTGCTCCTTCTTGACGAGCAAGTCGGCGGCCTCCAGGTTCTGAAAGACGGCAGCTGGGTCG
ACGTGCCCGTGCTGGGCGACGGCCGACACCAGCTGCTAGTCGTCGTCGGCGATGAGATGGAGATTACGAGCAACGCGGCG
TTCAGGGCGCCGATACACAGGGTGATGGCGCCGGGGGAGGAGGCGGAGCGGGTGTCGCTGGCGGTGTTCTACCAGCCGGA
GCCGGACAGGGTGCTCGAGCCGTCGCCCGAGCTGGTCGACGGGGAGCGGCCGGCGATGTACAAAAAGCTACAGGCCAAGG
TCTTCGCCGACGGCTTCTGGGACGCGTTCGCGCTCGGGGAACGCACCATCGACTTCCTCAAGGTCAAGGTCGACGCC

Alignment

ORF - retro_hvul_91 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 83.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IPIVDVSRLAMPDDVEESAKLRSALQSWGLFVVTGHGMPTELLDEILEATRKFFHLPPEEKQKCGNVID-
          IP.VDV.RLA...D..E..KLRSAL.SWGLF.VTGHGM....LD.IL.A.R.FFHLP.E.KQ...NV.D.
Retrocopy IPTVDVDRLA-DADAGEADKLRSALASWGLFAVTGHGMTDPFLDAILGAARGFFHLPMEAKQEYRNVVDA

Parental  ---GVSFQNEGYGIDRIDSDEQVLDWCDRLWLQLQPEDERRLQFWPQH---LRELLHEYTLESGRVTMDV
          ...G..FQ.EGYG.DR.D.DEQVLDWCDRL.LQ..P.D.R.L.FWP.H...L.ELL.E...E...V...V
Retrocopy DDGGRKFQPEGYGVDRVDTDEQVLDWCDRLYLQVRPDDARQLRFWPTHPSDLAELLKEFSVEGEKVAKLV

Parental  LKAMAKLLNQEEGFFIDMVGERFKSYSRFTYYPPCPRPDLVNGLKPHTDNSVITLLLMDKDVGGLQVLKD
          ..AMA..L..EEGFF.D.VGER..SY.RFTYYPPCPRPDLV.GLKPHTDNSV.T.LL.D..VGGLQVLKD
Retrocopy VTAMARCLGFEEGFFLDKVGERMPSYARFTYYPPCPRPDLVHGLKPHTDNSVVTVLLLDEQVGGLQVLKD

Parental  GNWVDVPVLG---HDLLVVVGEGMEIVSNAIFKAPWHRVVTSADK-ERMSLAMFYQPEPERIIGPPGALV
          G.WVDVPVLG...H.LLVVVG..MEI.SNA.F.AP.HRV.......ER.SLA.FYQPEP.R...P...LV
Retrocopy GSWVDVPVLGDGRHQLLVVVGDEMEITSNAAFRAPIHRVMAPGEEAERVSLAVFYQPEPDRVLEPSPELV

Parental  HEKRPPMFKKCLVQTLADGYWDAFAVGDRTVDFLNVRINA
          ...RP.M.KK......ADG.WDAFA.G.RT.DFL.V...A
Retrocopy DGERPAMYKKLQAKVFADGFWDAFALGERTIDFLKVKVDA

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_91 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
Aegilops tauschii	F775_08453	1 retrocopy	retro_atau_61,
Hordeum vulgare	MLOC_4579	1 retrocopy	retro_hvul_90,
Hordeum vulgare	MLOC_36995	1 retrocopy	retro_hvul_91 ,