RetrogeneDB ID: retro_sita_9

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 6:5192808..5193684(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si015338m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si014171m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_9
ATGGCTGATCACACCACGATGAGTAGTGAAGATCAGAGGCCGGTGGCGATCAGCGTGTGCTCGACGCCGAGCGACGACAG
GAGCCTCGCCGGCGCCGGCGCCGGCGCCGTGGCCTCCACGCCGAGATCGTCCAAGCTGGTGCCTCTCGATTCACTGCAGA
AACTGATGCTCAAGTCGCCGCTGGCTCCAGTCCAAGACGAGCCAGCACCGGTGCCGCTGGTGAAGAAGGTGGCGGCGGAG
TTCATCGGCACGTTCATCCTCATGTTCACGGTGGTGTCCGCCATCGTTGCCGACGCGCACCAGCACGGCGGCGGCGGCGG
CGCGGGGGGCGTCCTCGGCATCGCGGCGGCGGCGGGGCTCGCGGTGGTGGCGGTGGTGCTCGCCGTCGTGGACGTGTCGG
GGTCCCACCTGAACCCGGCCGTGAGCATCGCCATGGCCGCGTTCGGGCACCTCCCGCGCGCCCACGTGGCGCCCTACGCC
GCCGCGCAGACGCTGGGGTCCGCCGCCGCCACGTTCCTGGCGAAGGGGATGTACCGCCCCGCCGACCCCGGCGTGATGGC
GACGGTGCCCCGCGGCGGCGCCGTTGCCGAGGCGTTCTTCGTCGAGCTGGCGCTCACGTTCGTGCTCGTGTTCGTCATCG
CCGCCGTCGCCACCGACCCGGCGTCGAGCAAGGAGGCCGTCGCCGTCTCGATCGCGGCGGCGATCACGATGAACGCCCTC
GTCGGAGCGTCGTGGACGGGGCCGTCGATGAACCCGGCGAGGACGATCGGGGCGGCGGTGGCGACGGGGAAGTACAAGGA
CATCTGGGTCTACCTGGTGGCGCCGCCGCTGGGCGCCATCGCGGGAGCCGGCACCTACACACTCATCAAGCCCTGA

Alignment

ORF - retro_sita_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.64 %
• Parental protein coverage: 72.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPLIKKVVAEFLGTFILIFTVLSTIIMN-EQHD---GVESLLGIATSAGLAVTVLVLSLIHISGCHLNPA
          VPL.KKV.AEF.GTFIL.FTV.S.I.....QH....G....LGIA..AGLAV...VL.....SG.HLNPA
Retrocopy VPLVKKVAAEFIGTFILMFTVVSAIVADAHQHGGGGGAGGVLGIAAAAGLAVVAVVLAVVDVSGSHLNPA

Parental  VSIAMTVFGHLPLAHLLPYVTAQILGSIAASFSVKGIYHPVNPGI-ATIPKLGTT-EAFFLEFITTFVLL
          VSIAM..FGHLP.AH..PY..AQ.LGS.AA.F..KG.Y.P..PG..AT.P..G...EAFF.E...TFVL.
Retrocopy VSIAMAAFGHLPRAHVAPYAAAQTLGSAAATFLAKGMYRPADPGVMATVPRGGAVAEAFFVELALTFVLV

Parental  FIITALATDPNAVKELIAVAVGATIMMNALVAGPSTGASMNPARTLGPAIATGRYTQIWIYMVATPLGAV
          F.I.A.ATDP...KE..AV...A.I.MNALV....TG.SMNPART.G.A.ATG.Y..IW.Y.VA.PLGA.
Retrocopy FVIAAVATDPASSKEAVAVSIAAAITMNALVGASWTGPSMNPARTIGAAVATGKYKDIWVYLVAPPLGAI

Parental  AGTGAYVAIK
          AG.G.Y..IK
Retrocopy AGAGTYTLIK

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_9 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Setaria italica	Si014171m.g	1 retrocopy	retro_sita_9 ,