RetrogeneDB ID: retro_hvul_42

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:18132938..18133796(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_80447
• Aliases: None
• Description: None

Sequence

>retro_hvul_42
TACAGGAGCACTGGAGCTGAGGATGTGGCGATAAAGATTCTCTACTGCGGGATATGCCACTCTGACCTGCACAGCATTAA
GAACGAGTGGAAAAACGCTAGGTACCCGATGATCCCTGGGCACGAGATCGCCGGCGAGGTCAGCGAGGTGGGCAAGAAGG
TGACCAGGTTCGCGGCCGGCGACCGCGTGGGCGTCGGGTGCATGGTGAACTCGTGCGGGTCGTGCGAGAGCTGTGCCAAG
GGCTGCGAGAACCACTGCCCGGCCATGGCCTTCACCTACAACTCGTTCGACGACAGCGGCAGCGGCACCAACGCCGTCAC
CTACGGCGGCTACTCAAGCATGGTGGTGGTGAAGGAGCGCTTCGTTGTCCGGTTCCCGGAAGCCATGCCGCTGGACAAGG
GCGCCCCGCTGCTCTGCGCCGGCATCACCGTGTACAGCCCCATGAAGCACCACGGGCTCAACATCCCCGGGCTGCACCTC
GGCGTTGTGGGGCTGGGCGGGCTGGGCCACATGGCCGTCAAGTTCGGCAAGGCGTTTGGGATGAAGGTAACGGTGATCAG
CTCGTCGCCCGGGAAGAAGGAGGAGGCCCTCGGGCGGCTCGGCGCCGACGCGTTCGTCGTCAGCAACAACGCCGACGAGA
TGAAGGCCGCGATGAGCACCATGGATGGCATCATCAACACCGTGTCTGCAAACATGCCCATAGCCCCTCTCCTCGGCTTG
CTCAAGCCCAACGGCAAGATGGTCATGGTCGGCCTCCCGGAGAATTCCATCCAGCTCCCTCCCTTCGCTCTCGTTGCCAG
TAAGTCACTCACTAGTTCGTCAACAGTGTCTTTGTTGCAATTACTACAAGAAATCATC

Alignment

ORF - retro_hvul_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.02 %
• Parental protein coverage: 81.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FRSTGDDDVMIKILYCGICHSDLHSIKNDWKNAKYPMIPGHEIAGEVTEVGKNVTKFKAGDRVGVGCMVN
          .RSTG..DV.IKILYCGICHSDLHSIKN.WKNA.YPMIPGHEIAGEV.EVGK.VT.F.AGDRVGVGCMVN
Retrocopy YRSTGAEDVAIKILYCGICHSDLHSIKNEWKNARYPMIPGHEIAGEVSEVGKKVTRFAAGDRVGVGCMVN

Parental  SCQSCESCDKGFENHCPGIIFTYNSVDRDGT----VTHGGYSSMVVVHERFVVRFPDAMPLDKGAPLLCA
          SC.SCESC.KG.ENHCP...FTYNS.D..G.....VT.GGYSSMVVV.ERFVVRFP.AMPLDKGAPLLCA
Retrocopy SCGSCESCAKGCENHCPAMAFTYNSFDDSGSGTNAVTYGGYSSMVVVKERFVVRFPEAMPLDKGAPLLCA

Parental  GITVYSPMKYHGLNVPGLHLGVLGLGGLGHVAVKFGKAFGMKVTVISSSPGKKQEALERLGADAFVVSKD
          GITVYSPMK.HGLN.PGLHLGV.GLGGLGH.AVKFGKAFGMKVTVISSSPGKK.EAL.RLGADAFVVS..
Retrocopy GITVYSPMKHHGLNIPGLHLGVVGLGGLGHMAVKFGKAFGMKVTVISSSPGKKEEALGRLGADAFVVSNN

Parental  ADEMKAAVSTMDGIINTVSANIPMAPLLGLLKPNGKMIMVGLPEQPIEVPPFALVARNKTLAGSCIGGMR
          ADEMKAA.STMDGIINTVSAN.P.APLLGLLKPNGKM.MVGLPE..I..PPFALVA.......S......
Retrocopy ADEMKAAMSTMDGIINTVSANMPIAPLLGLLKPNGKMVMVGLPENSIQLPPFALVASKSLTSSSTVSLLQ

Parental  DTQEML
          ..QE..
Retrocopy LLQEII

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_42 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_80447	2 retrocopies	retro_hvul_34, retro_hvul_42 ,