RetrogeneDB ID: retro_sita_20

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 2:293891..294878(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si030497m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si036628m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_20
ATGGCCACCGGCAGCAGCAGCGTAAGCCCCGCGGCGGCGGCGCTCCTGGTGCTGGCAGCGAGCGCCACGGTGTGCGCGGC
GCAGCTCCGGCGCGACCACTACGCCGGCGTGTGCCCGGACGTGGAGTCCATCGTGCGCGGCGCCGTGGCCAAGAAGTATC
GGGAGACGTTCATCACGGTGGGCGCCACGTTGCACCTCTTCTTCCACGACTGCTTCGTCACCGGCTGCGACGCCTCCGTG
CTCGTGGCGTCCACGCCCAACAACACCGCCGAGAAGGACCACCCCGTGAACCTCGCCCTCGCCGGGGACGGCTTCGACAC
CGTCATCCGCGCCAGGGCCGCCGTCGACGCCGTGCCGCGGTGCCGGGGCCGTGTCTCCTGCGCCGACGTCCTCGCCATGG
CCACCCGGGACGCCATCGCGCTCGCCGGCGGGCCCTCGTACGCGGTCGAGCTCGGCCGGCTCGACGGCCTGAGCTCCACG
GCGAGCAGCGTCGACGGCAAGCTCGCGCCGCCGTCGTTCAACCTGGACCAGCTCACCGCGCTGTTCGCCACCAACGGGCT
GTCGCGGACCGACATGATCGCGCTCTCGGCGGGGCACACGGTGGGGTTCGCGCACTGCAGCACCTTCGCCGGCCGGATCC
AGGGGGCGGCGGCGCCGGACCCGACGCTGAACCGGAGCCTTGCGGCGCGGCTGCGGGAGTGGTGCCCGGCGGGGGTGGAC
CCGCGGATCGCCGTCACCATGGACGTGGTCACGCCGCGGGTGTTCGACAACCAGTACTTCAAGAACCTGCAGGACGGGAT
GGGCCTGCTCGCGTCCGACCAGGTGCTGTACACGGACCCGAGGTCCAGGCCCACGGTTGATGCCTGGGCCAAGAGCAGCG
TGGCGTTCAGCCAAGCCTTCGTGACTGCAATCACCAAGATGGGCCGGATCGGGGTCAAGACTGGGGCCCAAGGGAACATC
CGCCGCAACTGCGCAGTGCTCAATTGA

Alignment

ORF - retro_sita_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.19 %
• Parental protein coverage: 97.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAFLAALAAAAGVAAQLRQDYYAAVCPDLESIVRDAVSQKVQDQPVAVGATIRLFFHDCFVEGCDASVIM
          AA.L...A.A...AAQLR.D.YA.VCPD.ESIVR.AV..K.......VGAT..LFFHDCFV.GCDASV..
Retrocopy AALLVLAASATVCAAQLRRDHYAGVCPDVESIVRGAVAKKYRETFITVGATLHLFFHDCFVTGCDASVLV

Parental  VSTGNNTAEKDHPSNLSLAGDGFDTVIKAKAAVDAVPACTNQVSCADILALATRDVIALAGGPSYAVELG
          .ST.NNTAEKDHP.NL.LAGDGFDTVI.A.AAVDAVP.C...VSCAD.LA.ATRD.IALAGGPSYAVELG
Retrocopy ASTPNNTAEKDHPVNLALAGDGFDTVIRARAAVDAVPRCRGRVSCADVLAMATRDAIALAGGPSYAVELG

Parental  RLDGLVSLSTNVDGKLPPPSFDLDQLTTLFAAKNLSQADMIALSGAHTLGFAHCNTFAGRIQPESV-DPT
          RLDGL.S....VDGKL.PPSF.LDQLT.LFA...LS..DMIALS..HT.GFAHC.TFAGRIQ.....DPT
Retrocopy RLDGLSSTASSVDGKLAPPSFNLDQLTALFATNGLSRTDMIALSAGHTVGFAHCSTFAGRIQGAAAPDPT

Parental  MNATYAADLQAACPAGVDPNIALQLDPVTPQAFDNQYFVNLVNGRGLFTSDQVLYSDARSQPTVVAWAQN
          .N...AA.L...CPAGVDP.IA...D.VTP..FDNQYF.NL..G.GL..SDQVLY.D.RS.PTV.AWA..
Retrocopy LNRSLAARLREWCPAGVDPRIAVTMDVVTPRVFDNQYFKNLQDGMGLLASDQVLYTDPRSRPTVDAWAKS

Parental  ATDFEQAFVDAMTKLGRVDVKTDPSLGNIRRDCAFLN
          ...F.QAFV.A.TK.GR..VKT....GNIRR.CA.LN
Retrocopy SVAFSQAFVTAITKMGRIGVKTG-AQGNIRRNCAVLN

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_20 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	Si036628m.g	1 retrocopy	retro_sita_20 ,