RetrogeneDB ID: retro_sita_39

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 2:47244532..47245141(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si032185m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si023259m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_39
ATGGGTGAAGAGTGCAAGGAAGCCGCCGGCGGCGCCGGCGCTGGCCGTGCCGCCGTGGAGGGCCCCGTCGACCCGGCCGA
CTCGGCGAAGCTGTACGAGGACGTGCCCCCGATGCCGCTGATGGCGCTCAACCACATATCCCGCCTGTGCAAGTCCGTCG
ACGACTCCGTCCGGTTCTACGTCAAGGCCCTCGGCTTCGTCCTCATCCACCGCCCGCCGGCTCTCGACTTCTCCGGCGCA
TGGCTGTTCAACTACGGGGTGGGCATCCACCTCGTCCAGCGCGACGACGCGCGGAGGGCCCCCGACGTGAGCCCCGCCGG
CGAGCTGGACCCCATGGACAACCACATCTCGTTCCAGTGCGAGGACATGGGGATGATGGAGCGGCGGCTGCGGGAGATGC
GGATCAGGTACATGAAGCGGACCATCAACGAGGAGGAGGGCTCCCCCATCGACCAGCTCTTCTTCAAGGACCCCGACGGG
TTCATGATCGAGATCTGCAACTGCGAGAACCTCGAGCTCGTCCCCGCCGGCGCCCTCGGACGCCTCAGGCTCCCGCGCGA
CCGCCACAACCCGCCCGTCCGGATGGTCGACGGCGGCGGCGGCGAGTAG

Alignment

ORF - retro_sita_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.97 %
• Parental protein coverage: 65.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPLASLNHISIVCRSVEESLSFYTDVLGFVPIRRPGSFDFDGAWLFNYGIGIHLLQSEDPGSLPE---KR
          .PL..LNHIS..C.SV..S..FY...LGFV.I.RP...DF.GAWLFNYG.GIHL.Q..D....P......
Retrocopy MPLMALNHISRLCKSVDDSVRFYVKALGFVLIHRPPALDFSGAWLFNYGVGIHLVQRDDARRAPDVSPAG

Parental  EINPKDNHISFQCESMAAVERRLKEMGIPYVQRCV-EEGGINVDQIFFHDPDGFMIEICNCDNLPVIP
          E..P.DNHISFQCE.M...ERRL.EM.I.Y..R...EE.G...DQ.FF.DPDGFMIEICNC.NL...P
Retrocopy ELDPMDNHISFQCEDMGMMERRLREMRIRYMKRTINEEEGSPIDQLFFKDPDGFMIEICNCENLELVP

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_39 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G80160	1 retrocopy	retro_atha_15,
Brassica oleracea	Bo2g096220	1 retrocopy	retro_bole_1,
Brassica rapa	Bra008491	1 retrocopy	retro_brap_10,
Arabidopsis lyrata	fgenesh1_pm.C_scaffold_2001978	1 retrocopy	retro_alyr_14,
Medicago truncatula	MTR_2g103490	1 retrocopy	retro_mtru_44,
Setaria italica	Si023259m.g	1 retrocopy	retro_sita_39 ,