RetrogeneDB ID: retro_hvul_27

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:428249567..428250392(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MLOC_67686
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_52823
• Aliases: None
• Description: None

Sequence

>retro_hvul_27
ATGGCCGGCGTCGTGGTGGTGTTCGACTTCGACAAGACCATCATCGACGTCGACAGCGACAACTGGGTCGTCGACGGCCT
GGGCGCCACCGAGCTCTTCGACCGCCTGCTGCCCACCATGCCGTGGAACACCCTCATCGACACCGTTATGGGGGAGCTGC
ACGCGCAGGGCAAGACCCTCCGCGACGTCGCCGACGTGCTCCGGGCCGCGCCCATCGACCCGCACGTCGTCGCCGCCATC
AGGGCCGCCTACAGCCTCGGCTGCGACCTCAGGGTCCTCAGCGACGCCAACCGCTTCTTCATCGAGGCCGTCCTCGACCA
CCACGGCCTCCGGGGCTACTTCTCCGAGATCAACACCAACCCCAGCCGCGTCGACGCCGACGGCCGCCTCCGCATCGCGC
CGCACCACGACTTCCACGCCGGCCCGCACGGCTGCGGCCTCGGCACCTGCCCGCCCAACATGTGCAAGGGCCAGGTGCTC
GACCGCATCCGCGCCTCCTCCGCCACGGCGGACGGCACGAAACGCTTCATCTACCTCGGCGACGGGCGCGGCGACTACTG
CCCGTCGCTGCGGCTCGCCAGGGAGGACTTCATGATGCCGCGCAAGGGATTCCCCGTGTGGGAGCTCATCTGCGAGAACC
CGGGACTGCTCCAGGCCGAGGTGCACCCATGGAGCGACGGCAAGGACATGGAGGAGACGCTGCTGCGGCTCATCAGCCGG
GTGCTCGTCGAGGAGAGCCAGCTGCTGCCGCTCGACTGCAAGCTCGAGTCGCTGCCGGTGGCCGTCCAGGACGGCATGCC
CATGCCGCTCGGCGTCAAGAACTGA

Alignment

ORF - retro_hvul_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.01 %
• Parental protein coverage: 97.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAVVVLFDFDKTIIQWDSDDWVITKLGAADAFKRLRPTMRWNSLMDRMMGELHAQGRSADDIRECLRSAP
          A.VVV.FDFDKTII..DSD.WV...LGA...F.RL.PTM.WN.L.D..MGELHAQG....D....LR.AP
Retrocopy AGVVVVFDFDKTIIDVDSDNWVVDGLGATELFDRLLPTMPWNTLIDTVMGELHAQGKTLRDVADVLRAAP

Parental  LDAHVLSAIRTASALGCDLKVVSDANSFFIATVLEHHGVLGCFSEINTNPARVDAQGRLRISPFHDPTSS
          .D.HV..AIR.A..LGCDL.V.SDAN.FFI..VL.HHG..G.FSEINTNP.RVDA.GRLRI.P.HD....
Retrocopy IDPHVVAAIRAAYSLGCDLRVLSDANRFFIEAVLDHHGLRGYFSEINTNPSRVDADGRLRIAPHHDFHAG

Parental  PHGCSM--CPDNMCKGKIIQRIQEADSAKN--KHFIYIGDGKGDYCPSLKLREGDYVMPKENYPLWNLIS
          PHGC....CP.NMCKG....RI..........K.FIY.GDG.GDYCPSL.L...D..MP....P.W.LI.
Retrocopy PHGCGLGTCPPNMCKGQVLDRIRASSATADGTKRFIYLGDGRGDYCPSLRLAREDFMMPRKGFPVWELIC

Parental  SDPQLIKAEVHPWCSDEDFGRILLKLVNKLITLHAQASQLDYKCEMSNPVSTELGHHQTLPVPN
          ..P.L..AEVHPW....D....LL.L.........Q...LD.K.E.S.PV....G....L.V.N
Retrocopy ENPGLLQAEVHPWSDGKDMEETLLRLISRVLVEESQLLPLDCKLE-SLPVAVQDGMPMPLGVKN

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_27 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA001283	1 retrocopy	retro_oind_8,
Brachypodium distachyon	BRADI2G42720	1 retrocopy	retro_bdis_19,
Zea mays	GRMZM2G035134	1 retrocopy	retro_zmay_14,
Hordeum vulgare	MLOC_52823	1 retrocopy	retro_hvul_27 ,
Oryza brachyantha	OB01G31280	1 retrocopy	retro_obra_4,
Oryza glumaepatula	OGLUM01G25430	1 retrocopy	retro_oglu_22,
Oryza meridionalis	OMERI01G19970	1 retrocopy	retro_omer_22,
Oryza nivara	ONIVA01G24910	1 retrocopy	retro_oniv_37,
Oryza punctata	OPUNC01G21870	1 retrocopy	retro_opun_7,
Oryza rufipogon	ORUFI01G24440	1 retrocopy	retro_oruf_27,