RetrogeneDB ID: retro_hvul_55

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:269480123..269480884(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_72010
• Aliases: None
• Description: None

Sequence

>retro_hvul_55
AAGGGTTACGCCATTAGTGTCATCGACAACTTCCACAACTCTGTCCCCGAGGCACTCGCCATATCCGCCAGATCGTCCGT
CCCGCCCTCTCCGCCCGCCTTCAGTTCATCTTTGGCGATCGGACGATCAAAGATGACCTGGAGAAGGTGTTTACCTCCAA
GAGGAATGACACCATGGTACACTTCGTCGGGCTGAAGGCGGTGGCGGAGAGTGTGGCATACGTGGCGATGTAGAACCGCA
ACAACATCGTATGCACCATCAACCTCTACAACGTCATGAAGAAGCACGGGTGCAAAAAGTTTGTGTTCTCATCGACGGAG
ACTCTGTACAGCCAGCGGAGAAGGTCCCCTACATCAAGGACTATCCCTCAAGGCACTTGACCCGTACAGCAGGACCAAGT
TGTACCTCGAGGAGATGTTGCACGACTAACAACACACGAACTGAGAGTGAAGGACGATCATGTTGCACTAATTCAACCCC
ATCGGCACCCACGAGAGTGGCGACATCAGGGAGGGCCCCAAGGGGGTCCCCAACAACCTGCTCCCCTACATCCAGCAGGA
GGCCATCGGCCTACGCCCCGAGCTCAACTTCTACGACCACGGTTACCGCTCCCATGATGGCACCACTGTTAGGGGCTAAA
TGAACGTCGTTGACCTCATTGACATCCACATCGTGGTGCTCGATAAGCTCTTTGCCACCCTGAAATTAGCTACGTGTTCT
AAAACCTAGGGACGGGGTGCGAGACTACAATGCTGGTGATG

Alignment

ORF - retro_hvul_55 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.11 %
• Parental protein coverage: 85.28 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KGYAVTAVDNFHNSVPEALD-RVRHIVGPALSARLQFIFGDLTIKDDLEKVFAAKRYDAVIHFAGLKAVA
          KGYA....DNFHNSVPEAL....R.IV.PALSARLQFIFGD.TIKDDLEKVF..KR.D...HF.GLKAVA
Retrocopy KGYAISVIDNFHNSVPEALA<HIRQIVRPALSARLQFIFGDRTIKDDLEKVFTSKRNDTMVHFVGLKAVA

Parental  ESVAHPEMYNRNNIVGTVNLYDVMKKHGCNKLVFSSSATVYGQ-PEKVPCVEDSP-LKALNPYGRTKLYL
          ESVA...M.NRNNIV.T.NLY.VMKKHGC.K.VFSS..T.Y.Q..EKVP...D.P.LKAL.PY.RTKLYL
Retrocopy ESVAYVAM*NRNNIVCTINLYNVMKKHGCKKFVFSSTETLYSQ<AEKVPYIKDYP<LKALDPYSRTKLYL

Parental  EEMLRDYQHANPEWRTILLRYFNPIGAHQSGDIGEDPKGVPNNLLPYIQQVAVGRRPELNVYGHDYRTRD
          EEML.D.QH.N.E.RTI.L..FNPIG.H.SGDI.E.PKGVPNNLLPYIQQ.A.G.RPELN.Y.H.YR..D
Retrocopy EEMLHD*QHTN*E*RTIMLH*FNPIGTHESGDIREGPKGVPNNLLPYIQQEAIGLRPELNFYDHGYRSHD

Parental  GTAVRDYIHVVDLADGHIAALEKLFAT-PDIGCVAYNLGTGRGTTVLEM
          GT.VR....VVDL.D.HI..L.KLFAT.P.I..V..NLGTG..TT.L.M
Retrocopy GTTVRG*MNVVDLIDIHIVVLDKLFAT<PEISYVF*NLGTGCETTMLVM

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_55 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_72010	1 retrocopy	retro_hvul_55 ,