RetrogeneDB ID: retro_hvul_45

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 1:428359287..428359893(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_10647
• Aliases: None
• Description: None

Sequence

>retro_hvul_45
GGCGCCGCCTCGGACCGGACCCTCGTCGACGGCTTCCGCGGCATCGGGGACATGGCCGACCGGCTCGGCCTCGTCGCCAC
CATCCGGGACCAGGCCAAGGAGACTTTCAAGAAGCTGGACGAAGCCAAGGGCGTCCCCCGCGGCCGGAACCGGGACTCGG
TCTACGCCGCCTGCCTCTACATCGCCTGCCGCAACCTCGGCATGCCGCGCACCTACAAGGAGCTCGCCTCCGTCACCGCC
GCCGGCCCCGCCGCCAAGAAGGACATCGGCAAGATGTCGACGCACATCAAGAAGCTCCTCGGCGAGGAGGACGGCCAGGT
GATGGACATCGGCGTCGTCAGCGCCTCGGACTACCTGCGCCGCTTCTGCTCGCGGCTCGGCCTGGGCAACCAGGACGTGC
GCGACGCGCAGGAGGCCGTCAGGAGGCTCGAGGAACGCCTCGACGTGCGCCGCAACCCCGAGTCCATCGCAGCCGCCATC
ATCTACATGGTCGTGCAGCGCGCCGGCGCCAGCAACTCCGTCAAGGACGTGTCCGTCGCCACCGGCGTCGCCGAGGGCAC
CATCAAGGAGGCGCACAAGGACCTCACCCCGCACGCCCAAATGCTC

Alignment

ORF - retro_hvul_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.95 %
• Parental protein coverage: 63.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSNPDRSLILAFRTIANMADRLGLVATIKDRANEIYKKVEDLKSI-RGRNQDAILAACLYIACRQEDRPR
          G...DR.L...FR.I..MADRLGLVATI.D.A.E..KK....K...RGRN.D...AACLYIACR....PR
Retrocopy GAASDRTLVDGFRGIGDMADRLGLVATIRDQAKETFKKLDEAKGVPRGRNRDSVYAACLYIACRNLGMPR

Parental  TVKEICSV--ANGATKKEIGRAKEFIVKQLEVEMGQSMEMGTIHAGDFLRRFCSTLGMNNTAVKAAQEAV
          T.KE..SV..A..A.KK.IG.....I.K.L..E.GQ.M..G...A.D.LRRFCS.LG..N..V..AQEAV
Retrocopy TYKELASVTAAGPAAKKDIGKMSTHIKKLLGEEDGQVMDIGVVSASDYLRRFCSRLGLGNQDVRDAQEAV

Parental  QRSEE-LDIRRSPISIAAAVIYMITQLSEDKKPLKDISLATGVAEGTIRNSYKDLYPYAARL
          .R.EE.LD.RR.P.SIAAA.IYM..Q........KD.S.ATGVAEGTI....KDL.P.A..L
Retrocopy RRLEERLDVRRNPESIAAAIIYMVVQRAGASNSVKDVSVATGVAEGTIKEAHKDLTPHAQML

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_45 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G36290	1 retrocopy	retro_bdis_39,
Aegilops tauschii	F775_29675	1 retrocopy	retro_atau_5,
Hordeum vulgare	MLOC_10647	1 retrocopy	retro_hvul_45 ,
Medicago truncatula	MTR_7g091230	2 retrocopies	retro_mtru_26, retro_mtru_3,
Sorghum bicolor	Sb02g031020	1 retrocopy	retro_sbic_35,