RetrogeneDB ID: retro_sita_28

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 2:43914067..43914523(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si031390m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si014486m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_28
ATGGGCCGCATGTACGGCCCCGGGAAGGGCATGTCCTCGTCGGTGCTGCCCTACGCTCGCTCCGCGCCCGGGTGGGTCAG
GTCGTCCGCGGCGGAGGTGGAGGACATGATCGTGCGCGCCGCCAAGAAGGGCCAGCAGCCGTCGCAGATCGGCACGCTTC
TCCGCGACGCGCACGGCGTGCCGCTGGTCCACGGCGTCACGGGCGGCAAGATCCTGCGCGTGCTCAGGGCCCGCGGCCTC
GCGCCGGAGGTGCCCGAGGACCTCTACTTCCTCATCAAGAAGGCCGTCGCGATCAGGAAGCACCTGGACAGGAACCGGAC
GGACGTGGACGCCAAGTTCCGCCTCATCCTCGTCGAGAGCAGGGTCCACCGCCTCGCCCGCTACTACCGCCGCGCCAAGA
AGATCCCCGCCTCCTGGAAGTACGAATCCACCGCCGCCAGCACTCTGGTGGCATGA

Alignment

ORF - retro_sita_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.17 %
• Parental protein coverage: 76.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRMHSRGKGISSSALPYKRTAPTWLKTPASDVDEMITKAAKKGQMPSQIGVLLRDQHGIPLVHSVTGSK
          MGRM...GKG.SSS.LPY.R.AP.W....A..V..MI..AAKKGQ.PSQIG.LLRD.HG.PLVH.VTG.K
Retrocopy MGRMYGPGKGMSSSVLPYARSAPGWVRSSAAEVEDMIVRAAKKGQQPSQIGTLLRDAHGVPLVHGVTGGK

Parental  ILRILKAHGLAPEIPEDLYFLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKRTKKLPPTWK
          ILR.L.A.GLAPE.PEDLYFLIKKAVAIRKHL.RNR.D.D.KFRLILVESR.HRLARYY.R.KK.P..WK
Retrocopy ILRVLRARGLAPEVPEDLYFLIKKAVAIRKHLDRNRTDVDAKFRLILVESRVHRLARYYRRAKKIPASWK

Parental  YESTTASTLVA
          YEST.ASTLVA
Retrocopy YESTAASTLVA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Setaria italica was not studied using RNA-Seq expression data.

ChIP-Seq

Setaria italica was not studied using ChIP-Seq data.

EST

Setaria italica was not studied using EST data.

TSS

Setaria italica was not studied using FANTOM5 data.

Lab

retro_sita_28 was not experimentally validated.

Homology

Retrocopy orthology:

Setaria italica 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
Brachypodium distachyon	BRADI3G13810	1 retrocopy	retro_bdis_42,
Setaria italica	Si014486m.g	1 retrocopy	retro_sita_28 ,