RetrogeneDB ID: retro_sita_18

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 9:22654590..22655445(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si036923m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si017990m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_18
ATGAATCCTAGTGAATCCATGGAGGCCGCAGGGGGTAAGAAGGACTACAAAGACCCTGCCCCGGCGCCGCTCGTGAACGC
CGGCGAGCTGGGCAAGTGGTCCCTGTACCGCGCCGTCATCACCGAGTTCGTGGCCACGTTGCTCTTCGTGTACGTCACGC
TGGCCACCGTGATCGGGCACAAGCGCCAGTCCGAGTCCCAGCCATGCGGCGGCGCCGGCGTGCTGGGCATCGCGTGGTCC
TTCGGCGGCATGATCTTCGTGCTCGTCTACTGCACCGCCGGCGTCTCCGGCGGCCACGTCAACCCGGCCGTCACCTTCGG
CCTTCTCCTCGCGCGCAAGGTCTCCCTGGTGCGCGCCGCGCTCTACATCGTCGCGCAGTGCCTGGGCGCCATCTGCGGCG
CGGGACTCGTCAGGGCCTTCCACGGCACCAGCAGCTACCTGCGCCACGGCGGCGGCGCCAACGAGCTCGCCGCCGGCTAC
TCCAAGGGGGCCGGGCTGGCCGCCGAGATCGTCGGCACCTTCGTCCTCGTCTACACCGTGTTCTCGGCCACCGACCCCAA
GCGCAAGGTCAGGGACACGCACGTCCCGGTGCTGGCGCCGCTGCCCATCGGGTTCGCGGTGTTCATGGTGCACCTGGCCA
CCATCCCCATCACCGGCACCGGCATCAACCCGGCCAGGAGCCTGGGGCCGGCCGTGGTGTACAACCAGCGGAAGGCCTGG
GAGGATCACTGGATGTTCTGGGTCGGCCCGCTCATCGGCTCCGCCGCCGCCATGGTCTACCACCAGCTGGTCCTCCGCGC
TGGCGCCGCTAAGGCCTTCGCGTCCTGGCGCAACAACAACCACACCGGAATCTGA

Alignment

ORF - retro_sita_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 93.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDYSDPPPAPLIDAEELTKWSLYRAAIAEFVATLLFLYITVATVIGYKHQTDAAASGPDAACGGVGILGI
          KDY.DP.PAPL..A.EL.KWSLYRA.I.EFVATLLF.Y.T.ATVIG.K.Q.....S.P....G..GI...
Retrocopy KDYKDPAPAPLVNAGELGKWSLYRAVITEFVATLLFVYVTLATVIGHKRQSE---SQPCGGAGVLGI---

Parental  AWAFGGMIFILVYCTAGISGGHINPAVTFGLFLARKVSLVRAVLYIIAQCLGAICGVGLVKGFQ-SAYFV
          AW.FGGMIF.LVYCTAG.SGGH.NPAVTFGL.LARKVSLVRA.LYI.AQCLGAICG.GLV..F.......
Retrocopy AWSFGGMIFVLVYCTAGVSGGHVNPAVTFGLLLARKVSLVRAALYIVAQCLGAICGAGLVRAFHGTSSYL

Parental  RYGGGANELSAGYSKGTGLAAEIIGTFVLVYTVFSATDPKRSARDSHVPVLAPLPIGFAVFMVHLATIPI
          R.GGGANEL.AGYSKG.GLAAEI.GTFVLVYTVFSATDPKR..RD.HVPVLAPLPIGFAVFMVHLATIPI
Retrocopy RHGGGANELAAGYSKGAGLAAEIVGTFVLVYTVFSATDPKRKVRDTHVPVLAPLPIGFAVFMVHLATIPI

Parental  TGTGINPARSLGAAVIYNNDKAWDDQWIFWVGPLIGAAIAAAYHQYVLRASAAK-LGSFRSN
          TGTGINPARSLG.AV.YN..KAW.D.W.FWVGPLIG.A.A..YHQ.VLRA.AAK...S.R.N
Retrocopy TGTGINPARSLGPAVVYNQRKAWEDHWMFWVGPLIGSAAAMVYHQLVLRAGAAKAFASWRNN

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_18 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	Si017990m.g	1 retrocopy	retro_sita_18 ,