RetrogeneDB ID: retro_hvul_10

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:559497990..559498737(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_5705
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_6463
• Aliases: None
• Description: None

Sequence

>retro_hvul_10
ATGGAGCAGCAGGAGGAGGCGCCGACGTCGACGACGACGGTGGCGCTGGCCACGTCACCCAAGCCGGCGCCGGCGAGCAA
CGGCTGCAAGAAGCTGCCCTCGCGGTTCCGGCGGGTGTGCGTGTTCTGCGGGAGCAGCCCGGGGAGGAAGCCGGCGTACC
AGCTGGCCGCCGTGCAGCTGGGGCAGCAGCTGGTGGAGCGCGGCATCGACCTGGTCTACGGCGGCGGCAGCGTGGGCCTC
ATGGGCCTGGTGTCCCGCGCGGTGCACGGCGGCGGCGGGCGCGTGACGGGCGTCGTGCCCCGGTCGGTGCTCCCGCGGGA
GCTCATCGGCGAGACGCCCGGCGGGGAGGAGGTGAAGGCCGTGTCCGGCATGCACCAGCGCAAGGCCGAGATGGCCCGCC
GCGCCGACGCCTTCGTGGCGCTCCCCGGCGGCTACGGCACGCTGGAGGAGCTGCTGGAGGTGATCACCTGGGCGCAGCTC
GGCATCCACGACAAGCCCGTGGGCCTGCTCAACGTGGAGGGGTACTACGACTCGCTGCTGGACTTCATCGACCGGGCCGT
CGACGAGGGGTTCGTGTCGCCGGCGGCGAGGCACATCATCGTCGCCGCGCCCACGCCCGGCGAGCTGCTGGCGGCGCTGG
AGGAGTACGCGCCGGCGCACCACGACGCGTCCGCCGTGAAGCTCAGCTGGGAGTCGTCCGTGGACACCATGGCATGCTCG
CCCACCAAGCCGGACATCTCGCGCTAG

Alignment

ORF - retro_hvul_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.0 %
• Parental protein coverage: 82.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSRFRRICVFCGSSKGKKTSYQDAAVELGEELVSRNIDLVYGGGSVGLMGLVSQAVYSGGRHVIGVIPKT
          PSRFRR.CVFCGSS.G.K..YQ.AAV.LG..LV.R.IDLVYGGGSVGLMGLVS.AV..GG..V.GV.P..
Retrocopy PSRFRRVCVFCGSSPGRKPAYQLAAVQLGQQLVERGIDLVYGGGSVGLMGLVSRAVHGGGGRVTGVVPRS

Parental  LMPREITGETVG--EVKEVAGMHQRKAEMARQSDAFIALPGGYGTLEELLEVITWAQLGIHDKPVGLLNV
          ..PRE..GET.G..EVK.V.GMHQRKAEMAR..DAF.ALPGGYGTLEELLEVITWAQLGIHDKPVGLLNV
Retrocopy VLPRELIGETPGGEEVKAVSGMHQRKAEMARRADAFVALPGGYGTLEELLEVITWAQLGIHDKPVGLLNV

Parental  DGYYDALLSFIDKAVEEGFIKPTARDIIVLAPTPNELLDKLEGYSPGHEEV-VPRTEWET
          .GYYD.LL.FID.AV.EGF..P.AR.IIV.APTP.ELL..LE.Y.P.H.........WE.
Retrocopy EGYYDSLLDFIDRAVDEGFVSPAARHIIVAAPTPGELLAALEEYAPAHHDASAVKLSWES

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_10 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA008655	1 retrocopy	retro_oind_31,
Oryza longistaminata	KN538764.1_FG025	1 retrocopy	retro_olon_22,
Hordeum vulgare	MLOC_6463	1 retrocopy	retro_hvul_10 ,
Oryza barthii	OBART02G24840	1 retrocopy	retro_obar_25,
Oryza glumaepatula	OGLUM04G18920	1 retrocopy	retro_oglu_16,
Oryza nivara	ONIVA02G27160	1 retrocopy	retro_oniv_19,
Oryza rufipogon	ORUFI02G26160	1 retrocopy	retro_oruf_28,