RetrogeneDB ID: retro_hvul_73

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:470269887..470270820(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_60985
• Aliases: None
• Description: None

Sequence

>retro_hvul_73
GCAATGCCGGTTTGGTTCGTCTCCCTGGCCGTACTCGGTGCCATGTACCTTTCCGCCACCTGCCTCCGCCTCGTCGTCCA
CCTTGCCCTCTGTCTCCGCCGTCCCATCGACCTTCGCCGCCACTACGGCTCGTGGGCGGTCGTCACCGGCCCAACCACGG
GACTGGGGAGATCCATGGCCATGGAGCTCGCCCGCCGTGGCATCAGCCTCTTCCTCCTCGACCTCGACGCAGCGAACCTT
CAATCCGTCTCGGCCGACATCCACGCGGCCCACCCCAGAGTGGAAACCAAGACCGTGGTCTTCGATCTCTCTCTCGTCGG
CACCGCCGCCGGCGACTAGGCGATGCGGCGGATCAAAGAGGACATAGAGGGGCTGGACGTGGGGCTACTGGTGAACAATG
CCGCCGTGAATCGGCCCGGCGCGCTTTACGTGCACGAGGCGGACGGGGATCGGCTGGCAAGGATGGTGCTGGTGAACGTG
ATGGCGCTCACGGAGGTGACGGCGGCGGTGCTGCCCGGGATGCTGGAGCGGGGGAGGGGCGCCATTGTCAACGTCGGGTC
GGGGTCCACCGTGGCCGTGCCCTCCTTCCCGCTCTACACCGTCTACAGCGCCACAAAACGGTACGTGCAACACCTGACGC
GGTGCCTCAACGTGGAGTACAAGCAAAAGGGCATCGACGTGCAGTGCCAGGTCCCGTTCTACGTGCACACCGGCATGCTG
TCGCCGGCAATAAAGGCGACGATGAGATTCCCGGCGTTCGTGGCGACCGCCGACGCGTACGCCCGGGACGCGGCGCGGTG
GATCGGCCACGGCACGCTCTGCGTGCCCGACGCGTCCCAGCAGCTGCAGTGGTTCCTCGCCGGCCTTGTCCCCGACGCCG
TTCACGACTGGTACCGCCTCCGGCAGCATCTCAAGCACAGGGCCATCCTCCGG

Alignment

ORF - retro_hvul_73 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 91.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AASVWFFFSLALLGALHVSAVSIRLLASLALCLRRPKDLRHRYGAWAVVTGPTSGIGRSMSLELARRGLN
          A..VWF..SLA.LGA...SA...RL...LALCLRRP.DLR..YG.WAVVTGPT.G.GRSM..ELARRG..
Retrocopy AMPVWFV-SLAVLGAMYLSATCLRLVVHLALCLRRPIDLRRHYGSWAVVTGPTTGLGRSMAMELARRGIS

Parental  LVLVGRDPAKLRDISETISGAHA-VQTKTVLFDFSLVSAAQGDEAMRRLREAVAGLDVGLLVNNAGVAKP
          L.L...D.A.L...S..I..AH..V.TKTV.FD.SLV..A.GD.AMRR..E...GLDVGLLVNNA.V..P
Retrocopy LFLLDLDAANLQSVSADIHAAHPRVETKTVVFDLSLVGTAAGD*AMRRIKEDIEGLDVGLLVNNAAVNRP

Parental  GAMYLHEADVEAWARMIRVNVLALTEVTAAVLPGMVRRGRGAVVNLGSGSASVLPSFPLYSVYAATKRYV
          GA.Y.HEAD....ARM..VNV.ALTEVTAAVLPGM..RGRGA.VN.GSGS....PSFPLY.VY.ATKRYV
Retrocopy GALYVHEADGDRLARMVLVNVMALTEVTAAVLPGMLERGRGAIVNVGSGSTVAVPSFPLYTVYSATKRYV

Parental  AEFSRSLAVEYGSSGIDVQCQVPFLVETNMVSSAVKANL-ILQFVLTPDAYAYAAVRWIGHGRLCVPNVA
          ....R.L.VEY...GIDVQCQVPF.V.T.M.S.A.KA......FV.T.DAYA..A.RWIGHG.LCVP...
Retrocopy QHLTRCLNVEYKQKGIDVQCQVPFYVHTGMLSPAIKATMRFPAFVATADAYARDAARWIGHGTLCVPDAS

Parental  HRFQGWYAGLFPDFVNDAFRLEKNRGQRAILR
          ...Q...AGL.PD.V.D..RL......RAILR
Retrocopy QQLQWFLAGLVPDAVHDWYRLRQHLKHRAILR

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_73 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_60985	2 retrocopies	retro_hvul_73 , retro_hvul_96,
Hordeum vulgare	MLOC_65044	1 retrocopy	retro_hvul_95,