RetrogeneDB ID: retro_hvul_56

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:478890758..478892126(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_68498
• Aliases: None
• Description: None

Sequence

>retro_hvul_56
TACTCCCCCAGCGGCATAGTGGTGCCGCCATGGCTGAACAAGGGCGACAACGCATGGCAGATGATTGCTGCGACGCTGGT
GGGGTTACAGAGCATGCCCGGCCTGGTGATCCTCTACGGCAGCATCGTGAAGAAGAAGTGGGCCGTGAACTCGGCATTCA
TGGCGCTCTATGCCTTCGCCGCCGTGTGGCTCTGCTGGGTCACCTGGGGCTACAACATGTCCTTCGGCCACAAGCTGCTC
CCCTTCTGGGGCAAAGCCCGGCCGGCGCTCGGGCAGCAGTTCCTCCTCATGCAGGCCGTCCTGCCGGAGTCCACCCACTT
ATTCAAGGACGGCAGCACCGAGACGCCATGGATCAATCCGAATTACCCCATGGCCACCATGGTCTATTTCCAGTGCGTCT
TCGCCGCCATCACGCTCATCCTCCTCGCCGGTTCGCTGCTGGGCCGCATGAACATCAGGGCGTGGATGATCTTCGTCCCG
CTCTGGCTCACCTTCTCCTACACCATCGGCGCCTTCTCGCTCTGGGGCGGAGGCTTCCTCTTCCAGTGGGGCGTCATGGA
CTACTCCGGCGGCTACGTCATCCACCTCTCCTCCGGGATCGCCGGGTTCACCGCCGCGTACTGGGTGGGGCCCAGGTCCA
CCAAGGACAGGGAGAGATTCCCGCCCAACAACGTGCTCCTCATGCTCGCCGGCGCCGGCATACTCTGGATGGGGTGGGCC
GGGTTCAACGGCGGTGACCCTTACGCCGCCAACCTCGACTCTTCCATCGCCGTGCTCAACACCAACATCTGCGCCGCAAC
CAGCCTCCTCGTCTGGACCTCCCTGGACGTCATCTTCTTCAAGAAGCCCTCCGTCATCGGCGCCGTCCAGGGCATGATCA
CCGGCCTCGTTTGCATCACGCCCGGCGCGGGTCTCGTCCAGGGGTGGGCGGCGATCGTGATGGGCGTCCTGTCCGGCAGC
ATCCCGTGGTTCACGATGATGATCGTGCACAAGCGCTCCAAGCTGCTGCAACGCGTGGACGACACGCTGGGCGTGTTCCA
CACCCACGCAGTGGCGGGGTTCCTCGGCGGCGTGACCACGGGGCTCTTCGCGGAGCCGACGCTGTGCAGCATGTTCGTGC
CGGTGACCAACTCCCGCGGCGCCTTCTACGGAGGCAGCGGCGGCATGCAGCTCCTGAAGCAGGTGGTGGGCGCGCTCTTC
ATCATCGGCTGGAACGTGGTGGCCACCAGCATCATCTGCCTCGTCGTCCGGCTCATCGTACCGCTGCGGATGCCGGAGGA
GGAGCTCGTCATCGGCGACGACGCGGTGCACGGCGAGGAGGCCTACGCGCTCTGGGGCGACGGCGAGAAGTACGACTCCT
CCAAGCAC

Alignment

ORF - retro_hvul_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.74 %
• Parental protein coverage: 84.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YTATSPAVPEWLNKGDNAWQLTAATFVGIQSMPGLVVLYGSIVKKKWAVNSAFMALYAYASSLLVWVLVG
          Y......VP.WLNKGDNAWQ..AAT.VG.QSMPGLV.LYGSIVKKKWAVNSAFMALYA.A...L.WV..G
Retrocopy YSPSGIVVPPWLNKGDNAWQMIAATLVGLQSMPGLVILYGSIVKKKWAVNSAFMALYAFAAVWLCWVTWG

Parental  FRMAFGERLLPFWGKAGVALTQDYLVGRAKLSATAR----GST--PLVEPFYPEATLVMFQFEFAAITLI
          ..M.FG..LLPFWGKA..AL.Q..L...A.L.........GST..P...P.YP.AT.V.FQ..FAAITLI
Retrocopy YNMSFGHKLLPFWGKARPALGQQFLLMQAVLPESTHLFKDGSTETPWINPNYPMATMVYFQCVFAAITLI

Parental  LLAGSVLGRMNIKAWMAFTPLWLMLSYTVGAFSLWGGGFLYHWGVIDYSGGYVIHLSSGIAGFTAAYWVG
          LLAGS.LGRMNI.AWM.F.PLWL..SYT.GAFSLWGGGFL..WGV.DYSGGYVIHLSSGIAGFTAAYWVG
Retrocopy LLAGSLLGRMNIRAWMIFVPLWLTFSYTIGAFSLWGGGFLFQWGVMDYSGGYVIHLSSGIAGFTAAYWVG

Parental  PRLKSDRERFSPNNILLMIAGGGLLWMGWAGFNGGAPYAANITASVAVLNTNVSAATSLLTWTCLDVIFF
          PR...DRERF.PNN.LLM.AG.G.LWMGWAGFNGG.PYAAN...S.AVLNTN..AATSLL.WT.LDVIFF
Retrocopy PRSTKDRERFPPNNVLLMLAGAGILWMGWAGFNGGDPYAANLDSSIAVLNTNICAATSLLVWTSLDVIFF

Parental  GKPSVIGAVQGMMTGLVCITPGAGLVQTWAAVIIGVFAGSVPWFTMMILHKKSALLMKVDDTLAVFHTHA
          .KPSVIGAVQGM.TGLVCITPGAGLVQ.WAA...GV..GS.PWFTMMI.HK.S.LL..VDDTL.VFHTHA
Retrocopy KKPSVIGAVQGMITGLVCITPGAGLVQGWAAIVMGVLSGSIPWFTMMIVHKRSKLLQRVDDTLGVFHTHA

Parental  VAGLLGGILTGLLATPELMTMESSVLGPKGAFYGG-GIKQVGKQLAGAAFVIAWNIVVTTLILLGIGLFV
          VAG.LGG..TGL.A.P.L..M...V....GAFYGG.G..Q..KQ..GA.F.I.WN.V.T..I.L...L.V
Retrocopy VAGFLGGVTTGLFAEPTLCSMFVPVTNSRGAFYGGSGGMQLLKQVVGALFIIGWNVVATSIICLVVRLIV

Parental  PLRMPDDQLMIGDDAAHGEEAYALWGDGEKFDATRH
          PLRMP...L.IGDDA.HGEEAYALWGDGEK.D...H
Retrocopy PLRMPEEELVIGDDAVHGEEAYALWGDGEKYDSSKH

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_56 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_68498	1 retrocopy	retro_hvul_56 ,