RetrogeneDB ID: retro_sita_52

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 4:15528584..15529521(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si017474m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_52
GCCTCGGCGCCCGCGGAGAAGAGCAAGAGCTTCGTCGCGGACCTCCTCCTGGGCGGGGCGTCGTCGGCGGTGTCCAAGAC
GGTGGCGGCTCCGGTCGAGCGCGTCAAGATGCTTCTTCAGAACCAGGAAGCGCTCATCCGCGCCGGCCGCCTCTGGTACC
CCTACGGAGGCATCGGCGACTGCTTCCGCCGCACCGTCCGGGAGGAGGGCGCCCTCTCGCTGTGGCGCGGCAACGGCGCC
AACGTCGCCCGCTACTTCCCCACGCAGGCGCTCAACTTCGCCTTCAAGGACTACTTCCGGGGCCTGCTCGCCTTCCGCAG
GGACACGGACGGCTACTGGCGGTGGTTCGCCGGGAACGTCGCCTCCGGCAGCGCCGTGGGGGCCACGTCGCTGCTCTTCG
TCTACTTACTCCCTCGACTACGCCCGGACGCGCCTCACCAACGACTACCGCGCGGCGAAGGGTTGCGGCGAGAGGCAGTT
CGCGGGGCTGGCCGACGTCTACCGCAAGACGCTCCGCTCCGACGGCGTCGCCGGCCTCTACCGCGGCTTCAACGTCTCGG
TGGTCGGGATCGTCGTCTACCGCGGCCTCTACTTCGGCATGTACGACTCCTTCAAGCCCGTGCTGCTCACGGGGAAGCTG
CAGGACAGCTTCCTCGCGAGCTTGGCGCTCGGCTGGATGATCACCAATGGCGCGAACCTGGCCTCGTACCCGCTTGATTC
CGTCCGGAGGAGGATGATGATGACCTCGGGGGAGGCCGTCAAGTATAAGGGCGCCATTGACGCCTTCGCTCAGATCATCA
AGAACGAGGACCCCAAGTCGCTGTTCAAAGGCGCCGGCGCCAACGTCCTCCGCGCCATCGCCGGCGCCGGCGCGCTTGCT
GGCTACGATCACCTGCAGCTGCTCTTCTTTGGCAAGAAGCTCGGCTCCGGTGGCGCC

Alignment

ORF - retro_sita_52 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.2 %
• Parental protein coverage: 80.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ANAPAEKGGKNFMVDFLMGGVSAAVSKTAAAPIERVKLLIQNQDEMIKAGRLSEPYKGIGDCFKRTIKDE
          A.APAEK..K.F..D.L.GG.S.AVSKT.AAP.ERVK.L.QNQ...I.AGRL..PY.GIGDCF.RT...E
Retrocopy ASAPAEKS-KSFVADLLLGGASSAVSKTVAAPVERVKMLLQNQEALIRAGRLWYPYGGIGDCFRRTVREE

Parental  GFSSLWRGNTANVIRYFPTQALNFAFKDYFKRLFNFKKDKDGYWKWFAGNLASGGAAGASS-LFF-VYSL
          G..SLWRGN.ANV.RYFPTQALNFAFKDYF..L..F..D.DGYW.WFAGN.ASG.A.GA.S.LF...YSL
Retrocopy GALSLWRGNGANVARYFPTQALNFAFKDYFRGLLAFRRDTDGYWRWFAGNVASGSAVGATSLLFV>TYSL

Parental  DYARTRLANDAKAAKGGGDRQFNGLVDVYRKTLKSDGIAGLYRGFNISCVGIIVYRGLYFGLYDSIKPVV
          DYARTRL.ND..AAKG.G.RQF.GL.DVYRKTL.SDG.AGLYRGFN.S.VGI.VYRGLYFG.YDS.KPV.
Retrocopy DYARTRLTNDYRAAKGCGERQFAGLADVYRKTLRSDGVAGLYRGFNVSVVGIVVYRGLYFGMYDSFKPVL

Parental  LTGNLQDNFFASFALGWLITNGAGLASYPIDTVRRRMMMTSGEAVKYKSSMDAFQQILKKEGPKSLFKGA
          LTG.LQD.F.AS.ALGW.ITNGA.LASYP.D.VRRRMMMTSGEAVKYK...DAF.QI.K.E.PKSLFKGA
Retrocopy LTGKLQDSFLASLALGWMITNGANLASYPLDSVRRRMMMTSGEAVKYKGAIDAFAQIIKNEDPKSLFKGA

Parental  GANILRAIAGAGVLSGYDQLQILFFGKKYGSGGA
          GAN.LRAIAGAG.L.GYD.LQ.LFFGKK.GSGGA
Retrocopy GANVLRAIAGAGALAGYDHLQLLFFGKKLGSGGA

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_52 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	Sb04g029750	1 retrocopy	retro_sbic_17,
Setaria italica	Si017474m.g	1 retrocopy	retro_sita_52 ,