RetrogeneDB ID: retro_hvul_58

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 3:549541403..549542000(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_53047
• Aliases: None
• Description: None

Sequence

>retro_hvul_58
GCGTCGACGCAGCAGCACCAGCACCAGCAGGCGGCGGCGGCCACGCTGAAGGATAACAGCAGCACGGAGGTGGAGAAGAA
GGAGGGCAACAAGGGGAGGCAGCCAAACTCCGGCAACGGTCTCGACCTGGACAACTACTCGTGGACGCAGCAGCTGCCGG
AGGTGAACATCTCCGTCCCCGTCCCTGAAGGAACGAAGGGAAGGTCCGTGGTCTGCGAGATCAAGAAGGACCACCTCAAG
GTCGGGCTCAAGGGCCAGCCCCCCATCATCGACGGCGAGCTCCACGAACCTGTCAAGGTGGAGGACTGCTTCTGGAGCAT
CGAGGATGGTAGGTCGCTGTCCGTACTGCTCACCAAGCGTAATCGGAGCGAGTGGTGGAAGTCCGTGATCAAGGGCGAGC
CGGAGATCGACACCCAGCGTGCCGAACCGGAGAGCAGCAAGCTCTCGGACCTGGACCCCGAGACGAGGCAGACCGTGGAG
AAGATGATGTTCGATCAGAGGCAGAAGCAGATGGGCCTGCCTACGAGCGAGGAGATGCAGAACCAGGACATGCTCAAGAA
GCTGTACCCGGACATGGACTTCTCCGGGATGAAGATG

Alignment

ORF - retro_hvul_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.29 %
• Parental protein coverage: 65.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAAEKEKRESSVVTEGRGGSTEVEKEEG-KANKPNAGNGLDMEKYSWTQQLSEVNVNVPVPEGTKSRFV
          A.............T.....STEVEK.EG.K...PN.GNGLD...YSWTQQL.EVN..VPVPEGTK.R.V
Retrocopy ASTQQHQHQQAAAATLKDNSSTEVEKKEGNKGRQPNSGNGLDLDNYSWTQQLPEVNISVPVPEGTKGRSV

Parental  VCEIKKDRLKVGLKGQPPIIDGELYKPVKVDDCFWSIEDGKALSILLTKHNQMEWWKSVIKGDPEVDTQK
          VCEIKKD.LKVGLKGQPPIIDGEL..PVKV.DCFWSIEDG..LS.LLTK.N..EWWKSVIKG.PE.DTQ.
Retrocopy VCEIKKDHLKVGLKGQPPIIDGELHEPVKVEDCFWSIEDGRSLSVLLTKRNRSEWWKSVIKGEPEIDTQR

Parental  VEPENSKLSELDPETRQTVEKMMFDQRQKQMGLPTSDEMQKQDMLKKFMSQHPEMDFSNVKM
          .EPE.SKLS.LDPETRQTVEKMMFDQRQKQMGLPTS.EMQ.QDMLKK.....P.MDFS..KM
Retrocopy AEPESSKLSDLDPETRQTVEKMMFDQRQKQMGLPTSEEMQNQDMLKKL---YPDMDFSGMKM

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_58 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_53047	1 retrocopy	retro_hvul_58 ,
Theobroma cacao	TCM_015401	1 retrocopy	retro_tcac_31,