RetrogeneDB ID: retro_hvul_76

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 5:22853536..22854523(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_58322
• Aliases: None
• Description: None

Sequence

>retro_hvul_76
ATGAAACAAATATTCAAACACCTCCCTCGGGACAGGCAAACTGTTCTCTTTTCTGCCACACAGACTAAAAGGGTTGAAGA
TTTTGCGAACCTTACATTTGGGAGAAATGAAGAAAGGCAACGAAAACTTGTGTATGTTGGAGTTGATGATTCTGAGTTAA
AGCCTACTGTTGAGGGCCTGCAGCAAGGCTACTGTGTCATCCCAAGCGAGGAAAGGTTTCTGGTTTTGTATGCTTTCCTA
AGAAGGATGCAGCTGAAGCAGAAGGTGAAGGTCATGGTGTTCTTTTCATCATGCAGCTCTGTCAAATTCCACGCAGAATT
GCTTAACTTCCTTGGGATAGAGTGTTACGATATCCATGGCCAACTGAAGCAGCAGAAACGCACCACTACATTCTTCCGAT
TTTCCAAGGAGGAAAAGGGCATCTTGCTATGCACTAATGTGGCGGCACGTGGGCTTGATATTCCTGATGTGGACTACATT
GTGCAGTTCGATCCTCCGGATGACCCAAAGGACTACATTCACAGAGTTGGTCGTACTGCCCGAGGTGATAAAGGCAAAGG
ACGTGCATTGTTGTTCTTACTACCAGAAGAAATGAAGTTGCTCATTTACCTACGGGTGTCCAATATTTCTCTGACTGAAT
ATACGTTCAGTGGAAAGCATGTGCCAAAACTGCAACCTCAACTTGAGAAGATTGTTGCTGAGAATTACTTCCTAAAGCAG
TCAGCGAAGGAAGCCTACAGGTCCTACCTTTTGGCATACAACTCGCACTCTATGAAAGACATTTTTGGTGTCCATCAACT
TGACCTCAAGAACGTTGCAACATCTTTCTGTTTTAATAGCCCTCCTAAAGTGAATCTGAACCTGGAGAGTAGTGCATCGA
AACACCGGAAGATGAGGAAAGTGGATGGTGGAAAGGGGCATGGAATTAGCCATTCAAGCCCCTATGGAAGGAGTGGCGGC
ATTGATCGCAGGCAGTTTGCAAGATTC

Alignment

ORF - retro_hvul_76 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKQIFKRLPQNRQTVLFSATQTKEVEDFAKLSFEKNEERKEKPVYISVDDGKSNATVEGLQQGYCVIPSD
          MKQIFK.LP..RQTVLFSATQTK.VEDFA.L.F..NEER..K.VY..VDD.....TVEGLQQGYCVIPS.
Retrocopy MKQIFKHLPRDRQTVLFSATQTKRVEDFANLTFGRNEERQRKLVYVGVDDSELKPTVEGLQQGYCVIPSE

Parental  KRFLVLYAFLKK---KQSKKVMVFFSSCSSVKFHAELLNFLQIECEDIHGKQKQQKRTTTFFNFCKADKG
          .RFLVLYAFL.....KQ..KVMVFFSSCSSVKFHAELLNFL.IEC.DIHG..KQQKRTTTFF.F.K..KG
Retrocopy ERFLVLYAFLRRMQLKQKVKVMVFFSSCSSVKFHAELLNFLGIECYDIHGQLKQQKRTTTFFRFSKEEKG

Parental  ILLCTNVAARGLDIPDVDYIVQYDPPDEPKDYIHRVGRTARGEKGKGSALLFLLPQELKFLIYLKAAKIS
          ILLCTNVAARGLDIPDVDYIVQ.DPPD.PKDYIHRVGRTARG.KGKG.ALLFLLP.E.K.LIYL....IS
Retrocopy ILLCTNVAARGLDIPDVDYIVQFDPPDDPKDYIHRVGRTARGDKGKGRALLFLLPEEMKLLIYLRVSNIS

Parental  LTEYEFNNKNVPNLQSHLENIVGENYFLNQSAKEAYRSYILAYNSHAMKDIFNVHDLDMKAVAASFCFKN
          LTEY.F..K.VP.LQ..LE.IV.ENYFL.QSAKEAYRSY.LAYNSH.MKDIF.VH.LD.K.VA.SFCF..
Retrocopy LTEYTFSGKHVPKLQPQLEKIVAENYFLKQSAKEAYRSYLLAYNSHSMKDIFGVHQLDLKNVATSFCFNS

Parental  PPKVNLDLESSASKRRKTRKVDGGARRHGINAANPYGRKGGDDNRQFARF
          PPKVNL.LESSASK.RK.RKVDGG...HGI....PYGR.GG.D.RQFARF
Retrocopy PPKVNLNLESSASKHRKMRKVDGG-KGHGISHSSPYGRSGGIDRRQFARF

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_76 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_58322	1 retrocopy	retro_hvul_76 ,