RetrogeneDB ID: retro_hvul_100

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 7:584438064..584439015(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_65439
• Aliases: None
• Description: None

Sequence

>retro_hvul_100
ATGACAGCCCATGACGCATACTCTTTCCTCGTGAACTGGCTGGACAAGTTCCCCCAGTTCAAGGGCCACGACCTGTACAT
CGCCGGCGAGAGCTACGCCGGCCACTACGTCCCGCAGCTCGCCGAGAAGATCGTCCACATGAACAAGAAGGCCGCGCGGG
CGCACAAGATCAACCTCAAGGGGATCCTGATCGGGAACGCCGCCATCGACGCCAGCTCCGACGACCGCGGCCTGGTCGAC
TACGCCTGGGACCACGCCGTGGTCTCTGACGAGGTCTACACCGCCGTCAAGAACAACTGCATGTTCCCCGACGACGGCGT
GGAGAGCGACGCCTGCGACCACGCATGGAACGACTTCTTCAACGCCATGAACGACATCGACCTCTACAGCCTCTACACCC
CCGCCTGCACCAAGTCCATGGTCAACTCCACCGCCTCCTCCCCACGCCGCCGCTCCAAGCTCGCCGGCGTCGGCACGCCG
CTCGGCAAGCTGCACCGTGGCGGCAGGCCCTACTACAACGCCTACGACCCCTGCGGGGACTACCACATCATCGACTACCT
GAACCGCCCCGACGTGCAGAAGGCGCTGCACGCCAACGTCTCCGGCGCGATCCCGTACCGTTGGGAGCCGTGCAGCGACG
CGCTGACCAACTGGACGGACGCGCCGGCGTCGACCCTGCCGGCCATCGGCAAGCTGGTGAAGGACGGGATACGGGTGTGG
GTGTTCAGCGGCGACACCGACGACCGCGTGCCGGTGACCTCGACGCGGCTCGCGCTGAAGAAGCTCGGGCTCGCGACGAA
GAAGGAGTGGAGGGAGTGGTTCACCAGCGACCAGGTGGGCGGGTACACGGTGGTCTACGACGGGCTCACCTTCGTCACCA
TCCGCGGCGCCGGGCACATGGTGCCCATGATCACGCCGGTGCAGGCCAGGCAGGTCTTCGCGCACTTCCTC

Alignment

ORF - retro_hvul_100 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.94 %
• Parental protein coverage: 89.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITAADAYVFLLNWFKRFPQYKHHEFYIAGESYAGHYVPQLSEKIFDGNKHGPKENRINFKGLMVGNALMD
          .TA.DAY.FL.NW...FPQ.K.H..YIAGESYAGHYVPQL.EKI...NK.......IN.KG...GNA..D
Retrocopy MTAHDAYSFLVNWLDKFPQFKGHDLYIAGESYAGHYVPQLAEKIVHMNKKAARAHKINLKGILIGNAAID

Parental  DETDQAGMVQYAWDHAVISDRVYSDVKAHCDFAMDNTTA-ACEQALEDYFAVYRLIDMYSLYTPVCTDS-
          ...D..G.V.YAWDHAV.SD.VY..VK..C.F..D.....AC..A..D.F.....ID.YSLYTP.CT.S.
Retrocopy ASSDDRGLVDYAWDHAVVSDEVYTAVKNNCMFPDDGVESDACDHAWNDFFNAMNDIDLYSLYTPACTKSM

Parental  --SSSSPLAKRVGVHGAAPKIFSKYHGWYMRPAGYDPCTTQYSEVYFNRPDVQAALHANVT-KMGYNWTH
          ..S..S....R....G..........G.......YDPC.......Y.NRPDVQ.ALHANV.....Y.W..
Retrocopy VNSTASSPRRRSKLAGVGTPLGKLHRGGRPYYNAYDPCGDYHIIDYLNRPDVQKALHANVSGAIPYRWEP

Parental  CSDVIGKWNDAVPSTLPIIRKLVAGGIRVWVFSGDTDGRIPVTATRLTLNKLGLKTVQEWTPWYDRLQVG
          CSD....W.DA..STLP.I.KLV..GIRVWVFSGDTD.R.PVT.TRL.L.KLGL.T..EW..W....QVG
Retrocopy CSDALTNWTDAPASTLPAIGKLVKDGIRVWVFSGDTDDRVPVTSTRLALKKLGLATKKEWREWFTSDQVG

Parental  GWTITYEGLTFVTIRGAGHEVPMHAPRQALSLFTHFL
          G.T..Y.GLTFVTIRGAGH.VPM..P.QA...F.HFL
Retrocopy GYTVVYDGLTFVTIRGAGHMVPMITPVQARQVFAHFL

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_100 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_65439	1 retrocopy	retro_hvul_100 ,