RetrogeneDB ID: retro_hvul_102

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: morex_contig_202999:165..662(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_10092
• Aliases: None
• Description: None

Sequence

>retro_hvul_102
CGCAATGAACTTCCTGGTGGATTTTATGGTTTGAAGATCGGTGAGCAGAATGGTGGAGAGCAAGCACATGAAGGGGGTTA
CCAGGTGGACAAGTGCCCGTATTCTGGCCTTGAAAATGTTGTATTTGTTCGAGGTTCAGGACCGCATGCTCTGCATTACG
ATGGGCTACCTGGTCACTCTATGAAGGAGATAATTGTAAGTCGAAAATGTGCACAGTCAGTTCTTCGAGGAGCAAAGGTG
TATGTACCTGGTGTTTTAGCTTGCAGTGCACATGTTGAAACGGTGATAAGATTGCAGTGTCAGTGGCTATTGAGCAACCT
GTTAAGGACGGTGGTTGGGCTGTTGGTAAAACACGAGGAATCGTTCTACAGGGGTCGCAGTCAGATGAACATTATGAAGA
GAGAAAGGGTTTGTACATTGGTCAAGGGTTAGCTGCAATGTCAAGGTCAGGAATATTTCGTGTTCTCCATCGAGTTGCAG
TACAGATGGCTGAGAGG

Alignment

ORF - retro_hvul_102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.82 %
• Parental protein coverage: 63.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QNELPGGFNGLKIGEQNGGEQAHEGSYQVDKCPYSGLENVLFVRGSGPHALHYDGQPGHSMKEIIVSRKC
          .NELPGGF.GLKIGEQNGGEQAHEG.YQVDKCPYSGLENV.FVRGSGPHALHYDG.PGHSMKEIIVSRKC
Retrocopy RNELPGGFYGLKIGEQNGGEQAHEGGYQVDKCPYSGLENVVFVRGSGPHALHYDGLPGHSMKEIIVSRKC

Parental  AESVLRGAQVYVPGVLACSAHVE-KGDKIAVSVAIEQPVKDSGWAVGITRGIVLQGSQSDAHYEERKGLY
          A.SVLRGA.VYVPGVLACSAHVE..GDKIAVSVAIEQPVKD.GWAVG.TRGIVLQGSQSD.HYEERKGLY
Retrocopy AQSVLRGAKVYVPGVLACSAHVE<NGDKIAVSVAIEQPVKDGGWAVGKTRGIVLQGSQSDEHYEERKGLY

Parental  IGQGIAAMSRTGIFRVLHGVAVEMTER
          IGQG.AAMSR.GIFRVLH.VAV.M.ER
Retrocopy IGQGLAAMSRSGIFRVLHRVAVQMAER

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_102 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_10092	5 retrocopies	retro_hvul_101, retro_hvul_102 , retro_hvul_43, retro_hvul_72, retro_hvul_83,