RetrogeneDB ID: retro_sita_32

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: scaffold_11:115893..116949(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si020696m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si012266m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_32
ATGGACGATGAGTCCAACCCGCCATTGATGACCACGTACAAGCATCTCTTGGACACCCACCCGCACCGCCGGCTGGATGC
CGTCGACGATCACAACAGCGGGTGCGTCCTCCCGGTGATCGACCTGGGCAGCCTGCAGCACGCACCAGAGCAGTGCCGGG
CGGCCATCGTGCGCGCGGCGTCGGAGTGGGGCTTCTTCCAGGTGACCAACCACGGCGTGCCGCAGCCGCTGCTGGACGAG
CTGCACGACGCGCAGGTCGCCGTGTTCCGGCGGCCATTCGAGCGCAAGCTGCGCGAGCCGCTGCTCGACTTCTCGCCGGA
GAGCTACCGCTGGGGCACGCCGACGGCCACGTGCCTGGAGCAGCTGTCGTGGTCGGAGGCCTACCACATCCCCATGATCA
CGCCGGCCGCCGCCGCCGCCGCCGGTGATGACGACAGGACCAGGCTAGTGATCGAGGAGGTGTCCACGGCGATGTCCAAG
CTGGCGCTGCAGCTGGCGGGGATCCTCGTCGCAGACCTGCGCGGCGACGAGGAGAAGGACATGGTGGCGCGGTGCACGCG
CAACACGTGCTTCCTGCGGCTGAACCGGTACCCGGCGTGCGGCGCGGCGACCGGCGCCTTCGGGCTGTGCCCGCACACCG
ACAGCGACTTCCTCACCATCCTGCACCAGGACGCCGTCGGCGGCCTGCAGCTCCTCAAGGCCGGCCGCTGGGTCGCCGTC
AAGCCCAACCCCGGCGCGCTCATCGTCAACGTCGGCGACCTCCTGCAGGCATGGAGCAACGACCGCTATCGGAGCGTCGA
GCACCGGGTCATGGCCAGCGCCGCGAGCGAGAGGTTCTCCGTCGCCTTCTTCCTCTGCCCCGCCTACGACACGCTCATCC
GCCCGCGCAGCACCACCTCTTGCTCCGGCGGCGGCGCTTCTCCTCCTCGATACAGGAGCTTCACCTTCGGCGAGTACCGG
AACCAGATCAAGGAAGACGTCAGGCTCACGGGCCGAAAGATCGGCCTGCAACGCTTCCGACTGCAGCAGCAGCTCCAAGG
TGGCGGCCCATTGTAA

Alignment

ORF - retro_sita_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.73 %
• Parental protein coverage: 69.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAREARAACAYAMARAASEWGFFQVTGHGVGRALLERLRAEQARLFRLPFETKARAGLLN---GSYRWGA
          S...A...C..A..RAASEWGFFQVT.HGV...LL..L...Q...FR.PFE.K.R..LL.....SYRWG.
Retrocopy SLQHAPEQCRAAIVRAASEWGFFQVTNHGVPQPLLDELHDAQVAVFRRPFERKLREPLLDFSPESYRWGT

Parental  PTATSLRHLSWSEAFHVPLASISGSGCDFGELGSLRGVMQEVADAMSRVAKTVAVALAGSLLQGHHAAAA
          PTAT.L..LSWSEA.H.P...........G.....R.V..EV..AMS......A..LAG.L.........
Retrocopy PTATCLEQLSWSEAYHIPMITPAAAAAA-GDDDRTRLVIEEVSTAMSKL----ALQLAGILVADLRGDEE

Parental  AAFPAGCDETTCFLRLNRYPACPFAPDTFGLVPHTDSDFLTVLCQDQVGGLQLMKDARWVAVKPHPDALI
          ....A.C...TCFLRLNRYPAC..A...FGL.PHTDSDFLT.L.QD.VGGLQL.K..RWVAVKP.P.ALI
Retrocopy KDMVARCTRNTCFLRLNRYPACGAATGAFGLCPHTDSDFLTILHQDAVGGLQLLKAGRWVAVKPNPGALI

Parental  VNIGDLFQAWSNNRYKSVEHKVVANAKAERFSAAYFLCPSYDS
          VN.GDL.QAWSN.RY.SVEH.V.A.A..ERFS.A.FLCP.YD.
Retrocopy VNVGDLLQAWSNDRYRSVEHRVMASAASERFSVAFFLCPAYDT

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_32 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G006964	1 retrocopy	retro_zmay_24,
Sorghum bicolor	Sb06g022880	1 retrocopy	retro_sbic_13,
Setaria italica	Si001573m.g	1 retrocopy	retro_sita_29,
Setaria italica	Si012266m.g	1 retrocopy	retro_sita_32 ,