RetrogeneDB ID: retro_hvul_41

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:428822801..428823854(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_70474
• Aliases: None
• Description: None

Sequence

>retro_hvul_41
GAGTACTACCACCTGGCCAAGGAGCAGGGGTACCGGAGCCGGGCGGCCTTCAAGCTGCAGCAGCTAGACGACCGCTTCCG
ATTCCTCCCGGCGGCGCGCGCCGTGCTCGATCTCTGCGCGGCGCCGGGAGGCTGGGTCCAGGTGGCCGTCGCCCGCGCCC
CCGCCGGCGCCTTCGTCGTCGGCGTCGACCTCGTGCCGATCCGCCCCGTCCGCGGCGCGCACTCGCTCACGGAGGACATC
ACCATCACCAGGTGCCGCTCCGCCGTGCGGAGGCTCATGGACTCCAGGGGGGTCGCCGTCTTCGACGTGGTCCTCCACGA
CGGCTCGCCCAACGTCGGCGGCGCGTGGGCGCAGGAGGCCACCGCGCAGTCCGCGCTCGTCATCGACGCGGTCCGCCTGG
CCACCGCGTTCCTCGCCCCCAAGGGCGCCTTCATCACCAAGGTCTTCAGGTCTCAGGATTACAGCGCCATCATGTTCTGT
CTGAAGCAGCTGTTTGATAAGGTCGAGGTGACTAAACCTCGAGCCAGTCGCGGCACATCCGCTGAAATTTACATCATCTG
TCTGAAGTACAAAGCCCCTGCAAAGATTCAACCAGAGCTTCTTGATATCAAGCACCTGTTCAGTGTGGATCCAGAGAAGA
GCACGCCTACGGATGTACTTGACACTAATAAGAATGCAAAGAAGAGAACTCGTGGTGGGTATGCGGCCGGAGTCACGGTA
CTGGAGAAAGTTGGCCTCGCATCAGATTTCATATGGTCCGAGGCGCAGAAACCACGGGAATTCCTTGGTTCTTTCACCAA
GATTTCATTTGATGATCCTGCGTCTCTGCCCATCGAAAACCATGAGCTCACCACGGATGAGGTAAAATGTCTTTGTGAGG
ATTTGCAGGTGCTGGATAAAAATAGCTTCAAGCATATCTTGAAGTGGCGCACACGCCTAAGGAATGCTCTGCCATCATCT
TCGCAAGTCACACCAAAAGCTGATGGTACTGCGACGAACACCAAGGTCAAAGGTGATGTTCAGCTTTTACAGGAAATGGA
AGAAATGGGTTCC

Alignment

ORF - retro_hvul_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.48 %
• Parental protein coverage: 83.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYYHLAKEQGYRSRAAFKLLQLDARFRFLPTARAVLDLCAAPGGWVQVAVNHAPVGAFVVGVDLVPIRPI
          .YYHLAKEQGYRSRAAFKL.QLD.RFRFLP.ARAVLDLCAAPGGWVQVAV..AP.GAFVVGVDLVPIRP.
Retrocopy EYYHLAKEQGYRSRAAFKLQQLDDRFRFLPAARAVLDLCAAPGGWVQVAVARAPAGAFVVGVDLVPIRPV

Parental  RGAHSLTEDITTSKCRSAVRKLMDSKGVASFDVVLHDGSPNVGGAWAQEATTQSALVIDAVRLATMFLAP
          RGAHSLTEDIT...CRSAVR.LMDS.GVA.FDVVLHDGSPNVGGAWAQEAT.QSALVIDAVRLAT.FLAP
Retrocopy RGAHSLTEDITITRCRSAVRRLMDSRGVAVFDVVLHDGSPNVGGAWAQEATAQSALVIDAVRLATAFLAP

Parental  KGAFITKVFRSQDYNAIMFCLKQLFEKVEVTKPNASRGTSAEIYIICLKYKAPAKIAPELLDIKHLFNVE
          KGAFITKVFRSQDY.AIMFCLKQLF.KVEVTKP.ASRGTSAEIYIICLKYKAPAKI.PELLDIKHLF.V.
Retrocopy KGAFITKVFRSQDYSAIMFCLKQLFDKVEVTKPRASRGTSAEIYIICLKYKAPAKIQPELLDIKHLFSVD

Parental  PEKKMPRDVLGTKKD--KRQREGYDEGVTVLRKVGLASDFIWSDAQTPLEFLGSVTEISFDDAASVPIKN
          PEK..P.DVL.T.K...KR.R.GY..GVTVL.KVGLASDFIWS.AQ.P.EFLGS.T.ISFDD.AS.PI.N
Retrocopy PEKSTPTDVLDTNKNAKKRTRGGYAAGVTVLEKVGLASDFIWSEAQKPREFLGSFTKISFDDPASLPIEN

Parental  HEITTDEIKNLCDDLRVLDKNSFKHILKWRIRIRKALSSSSQVTPKADGTATETKVNDDDQLLQEMEELT
          HE.TTDE.K.LC.DL.VLDKNSFKHILKWR.R.R.AL.SSSQVTPKADGTAT.TKV..D.QLLQEMEE..
Retrocopy HELTTDEVKCLCEDLQVLDKNSFKHILKWRTRLRNALPSSSQVTPKADGTATNTKVKGDVQLLQEMEEMG

Parental  S
          S
Retrocopy S

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_41 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_70474	1 retrocopy	retro_hvul_41 ,