RetrogeneDB ID: retro_hvul_31

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: morex_contig_90269:1175..2042(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_80395
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_54751
• Aliases: None
• Description: None

Sequence

>retro_hvul_31
CCGGAGAGCGTCGCCTTCGACGCCAAAGGGCACGGCCCATACAGCGGCGTCTCCGACGGCCGCGTGCTCAGGTGGAACGG
CGACGCGCTCGGCTGGTCGACCTACACCTACAACCCCGACTACAGCAGCGAGGCGTGCACGGCGTCCGTCTTCCGCCCGG
AGACGGCCACGGAGAGCCACTGCGGACGCCCGCTAGGCCTGCGGTTCCACCTCAAGTCCGGGTACCTGTACATCGCCGAC
GCCTACAAGGGGCTCATGAGGGTCGCGCCCGGCGGTGGGGAGGCGACTGTGCTGGTCACGGAGGTTGACGGCGCACCTCT
CCGCTTCACCAACGGCGTGGACGTCGACCAAGTCACCGGCGAGGTTTATTTCACAGACAGCTCCACCAACTTCAATAGGT
CGCAGCATGAGATGGTGACAAGAACCGGAGACTCGACGGGACGGCTAATGAGGTACGACCCACGGACGGGGAAGGCCGTC
GTGCTCCAGGCCGGCATCACTTACCCCAATGGTCTTGCCATCAGCGCTGATAGGACGCATCTCATCATCTCGTCGACCGG
GCCGTGTAAGCTGCTACGATACTGGATCAAGGGCTCCAAGGCGGGCACGATGGAGCTATTCGCCGACCTTCCTGGCTATC
CAGACAATGTAAGGCCCGACAAGAAAGGAGGATATTGGGTGGCACTACACCGTGAAAAGAATGAGCTCCCCTTTGGCATT
GATAGCCACTTGCTAGCCTTGAGGATTGATGCCCATGGAAAAATTACTGAAGAGATGAGGGGGCCCAAGAGCGTGAGGCC
GACCGAGGTGGTGGAGAGGAGAGGAGGCAAATTGTTCATGGGATCCGTCGAGCTTCGCTATGTCTCC

Alignment

ORF - retro_hvul_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.79 %
• Parental protein coverage: 69.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PESIVFDHRGGGPYTGVSNGRVLRWRGNRRHHGWTEFAHNYKHKTVAECAAK-KKLVEPESACGRPLGLQ
          PES..FD..G.GPY.GVS.GRVLRW.G.....GW.....N......A..A.........ES.CGRPLGL.
Retrocopy PESVAFDAKGHGPYSGVSDGRVLRWNGDAL--GWSTYTYNPDYSSEACTASVFRPETATESHCGRPLGLR

Parental  FHHASGDMYIADAYLGLMRVGRCGGLAEVVATETGGVPFNFLNGVDVDQETGDVYFTDSSTVYPRSEYMM
          FH..SG..YIADAY.GLMRV...GG.A.V..TE..G.P..F.NGVDVDQ.TG.VYFTDSST...RS...M
Retrocopy FHLKSGYLYIADAYKGLMRVAPGGGEATVLVTEVDGAPLRFTNGVDVDQVTGEVYFTDSSTNFNRSQHEM

Parental  VVLTGDATGRLMRYDPRTGNVTVLRSGLAFPNGVAVSADRTHLVVAETSSCRLLRHWLRGPAAGTTEVLA
          V..TGD.TGRLMRYDPRTG...VL..G...PNG.A.SADRTHL....T..C.LLR.W..G..AGT.E..A
Retrocopy VTRTGDSTGRLMRYDPRTGKAVVLQAGITYPNGLAISADRTHLIISSTGPCKLLRYWIKGSKAGTMELFA

Parental  DLPGYPDNVRPDGGGRGGYWVGMNRDKQWAESGTTANSMSAVRVVVDGGAT
          DLPGYPDNVRPD....GGYWV...R.K.....G.......A.R....G..T
Retrocopy DLPGYPDNVRPD--KKGGYWVALHREKNELPFGIDSH-LLALRIDAHGKIT

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_31 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_54751	1 retrocopy	retro_hvul_31 ,