RetrogeneDB ID: retro_hvul_68

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 4:13235000..13235585(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_73076
• Aliases: None
• Description: None

Sequence

>retro_hvul_68
TGTTGGGCCTTTTCAGTTGTGGCCGCGACCAAAGGCATTGTGAAGTTGAGCACAAGGAACCTTGTCTCTCTGTCGGAACA
AGAGGTAGTTGATTGTGACATTCATGGTGTAGATCAGGGTTGCGAACGTGGCGAGATAGACAATGCCTTCAAGTTCATCA
TCAAGAATGGCGACTTCACCACCGAGGCCAACTACCCCTACACGGCACAAGACGGACAATGCAAGACCAGCATTGCAAGC
AACAGTGTTGCAACCAATAAGGGCTACCAGGATGTGCCCACCAATGATGAATCTTCTCTTATCAAAGCCGTGGCTAACCA
GCCCGTGTCAGTTGTTGTTGACCGAGGGGATGTCATATTTCAACATTTCTCCGGAGGGGTAATGACCAGCTCCTGCGGCA
CTAATTTGGACCATGGAATAGCAGCGATTGGATATGGCATGACGAGTGACGGAACTAAGTATTGGCTAGTGAAAAACTCA
TGGGGCACGAAATGAGGCGAGAGCGGGTACCTCAGAATGGAGAAGGATATTTCTCAGGAGAGTGGTATGTGTGGCTTGGC
CATGCAACCTTCCTACCCCACCGAG

Alignment

ORF - retro_hvul_68 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.92 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CWAFSTIVAVEGINKIRTGKLVSLSEQELMDCD-NVNNQGCDGGLMDYAFQFIQKNG-ITTESNYPYQGE
          CWAFS...A..GI.K..T..LVSLSEQE..DCD.....QGC..G..D.AF.FI.KNG..TTE.NYPY...
Retrocopy CWAFSVVAATKGIVKLSTRNLVSLSEQEVVDCDIHGVDQGCERGEIDNAFKFIIKNGDFTTEANYPYTAQ

Parental  QGSCDQAKENALAVTIDGYEDVPANDESALQKAVAGQPVSVAIDASGQDFQFYSEGVFTGECSTDLDHGV
          .G.C..........T..GY.DVP.NDES.L.KAVA.QPVSV..D.....FQ..S.GV.T..C.T.LDHG.
Retrocopy DGQCKTSIASNSVATNKGYQDVPTNDESSLIKAVANQPVSVVVDRGDVIFQHFSGGVMTSSCGTNLDHGI

Parental  AAVGYGATRDGTKYWIVKNSWGEDWGEKGYIRMQRGVSQTEGLCGIAMQASYPTK
          AA.GYG.T.DGTKYW.VKNSWG...GE.GY.RM....SQ..G.CG.AMQ.SYPT.
Retrocopy AAIGYGMTSDGTKYWLVKNSWGTK*GESGYLRMEKDISQESGMCGLAMQPSYPTE

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_68 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G19707	2 retrocopies	retro_bdis_26, retro_bdis_41,
Zea mays	GRMZM2G099765	1 retrocopy	retro_zmay_16,
Hordeum vulgare	MLOC_73076	2 retrocopies	retro_hvul_23, retro_hvul_68 ,
Hordeum vulgare	MLOC_81876	2 retrocopies	retro_hvul_49, retro_hvul_92,
Oryza barthii	OBART11G08490	1 retrocopy	retro_obar_27,
Oryza glumaepatula	OGLUM05G09560	1 retrocopy	retro_oglu_31,
Oryza meridionalis	OMERI11G07520	1 retrocopy	retro_omer_2,
Setaria italica	Si026545m.g	1 retrocopy	retro_sita_27,