RetrogeneDB ID: retro_sita_8

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 6:186815..187457(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si015337m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si023150m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_8
ATGAGCGAGCCCGCGACCGTGATCCACATGGACGGCGGCAAGGCTCCTCCGACGACTGGTGATGCCGCAGGCAGCAGCAG
CAAGGCCGCTGGTCGTGGTCTCCCGCTGATCCTGCGGTCCAGCGGCGGCGGCGGGTTCCGGCGGTGCCTGGCGGTGATCG
ACTTTTTGCTGCGTGTGGCCGCGTTCGGGCCGACGCTGGCGGCGGCCATCTCGACGGGCACCGCCGACGAGCGGCTGTCG
GTGTTCACTCAGTTCTTCCAGTTCCACGCCCGTTTCGACGACTTCACGGCCTTCATCTTCTTCATGGTGGCCAACGCGGT
GGCGGCGGGGTACCTGGTGCTGTCGCTGCCCTTCTCCGCCGTGGGCATCGTCCGCCCCAAGGCCACCGGCGTGAGGGTGT
TCCTTCTCGTCTGCGACGTGCTGGTCATGTCCCTGCTGACGGCGGCCGGCGCCGCGGCAGCCGCCATCGTGTACGTGTCG
CACTGGGGCAGCCTGCGCGCCAACTGGGTGCCCATCTGCATGCAGTTCCACGGCTTCTGCCAGCGCACCAGCGGCGCCGT
CGTCGCCACCTTCCTCGCCGTCCTCGTCCTGCTCGTGCTCATCCTCATGGCCGCCTGCTCCATCCGACGACGCAGGCACT
AG

Alignment

ORF - retro_sita_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.17 %
• Parental protein coverage: 86.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APPATSSAVPAAAAATTAPRKTGVPFFRRADRGS---RCVALVDFVLRIAAFGPTLAAAIATGTSDETLS
          APP.T......AA.........G.P...R...G....RC.A..DF.LR.AAFGPTLAAAI.TGT.DE.LS
Retrocopy APPTTGD----AAGSSSKAAGRGLPLILRSSGGGGFRRCLAVIDFLLRVAAFGPTLAAAISTGTADERLS

Parental  VFTQFFQFRARFDDFPALLFFMVANAIAAGYLVLSLPFSAVVVLRPQAIGLRHLLLVCDTIIVAMLTAAA
          VFTQFFQF.ARFDDF.A..FFMVANA.AAGYLVLSLPFSAV...RP.A.G.R..LLVCD......LTAA.
Retrocopy VFTQFFQFHARFDDFTAFIFFMVANAVAAGYLVLSLPFSAVGIVRPKATGVRVFLLVCDVLVMSLLTAAG

Parental  AAAAAIVDLAHSGNLRANWVPICMQFHGFCQRTSGAVVASFLAVLVFVLLVILAAFAIRKR
          AAAAAIV...H.G.LRANWVPICMQFHGFCQRTSGAVVA.FLAVLV...L...AA..IR.R
Retrocopy AAAAAIVYVSHWGSLRANWVPICMQFHGFCQRTSGAVVATFLAVLVLLVLILMAACSIRRR

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_8 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
Sorghum bicolor	Sb06g033470	1 retrocopy	retro_sbic_31,
Setaria italica	Si023150m.g	1 retrocopy	retro_sita_8 ,