RetrogeneDB ID: retro_hvul_62

Retrocopy location

• Organism: Barley (Hordeum vulgare)
• Coordinates: 4:242687820..242688112(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MLOC_27966
• Aliases: None
• Description: None

Sequence

>retro_hvul_62
AACAGCACTGCCCCGGTTCAGTTCAGCAAGGAGACCAACTACCTCTATAATGTCCACTCGTGCTGGTTTTTGACCTGTCA
AACAAGAACACATGGTGCTAGTTGCTGAAAAGGAGATGACAGTGGTCCTCTTGACAACGAAGACGATGACGCAACAGACC
AAGCCTTCTGCGTTCTTCGCTCGCATGCACAAGGAGTTCCGCTAGATGGATAACGCTGTCAAGAACCAGGTCACTGGCAA
CTACTACATGACAAAACCCGCTCTTGCAAGGCTTTCAATTTACCGCAACTTG

Alignment

ORF - retro_hvul_62 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.47 %
• Parental protein coverage: 73.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NSNAKVQFSKEPNNLYNVHSYKY-SGLANKKT-VTVQPAAEKEMTVVLSTTKSKKQNKPAAFTHKTVMRK
          NS.A.VQFSKE.N.LYNVHS......L.NK.T........E.........T....Q.KP.AF.....M.K
Retrocopy NSTAPVQFSKETNYLYNVHSCWF<FDLSNKNT<MVLVAEKEMTVVLLTTKTMTQ-QTKPSAFFAR--MHK

Parental  EFRKMAKAVKNQVSDNYYRPDLTKPALARLSAVYRSL
          EFR.M..AVKNQV..NYY....TKPALARLS..YR.L
Retrocopy EFR*MDNAVKNQVTGNYY---MTKPALARLS-IYRNL

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_62 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_27966	2 retrocopies	retro_hvul_61, retro_hvul_62 ,
Triticum aestivum	Traes_3DL_E7983BF89	1 retrocopy	retro_taes_110,