RetrogeneDB ID: retro_sita_24

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 5:8250033..8251098(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si002029m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si001973m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_24
ATGGCGGCGACGACACCCTCCGAGCTGGAGCACAAGGCGAAGGAGGCCTTCTTCGACGACGACTTCGCCCTCGCCGCCGC
GCTCTACACGCAGGCCATCGCTGCGGGGGCCCCCGCCGCCGCGCTCTACGCCGATCGCGCCCAGGCCTACATCAAGATGG
GAGATTTCGCCGCGGCCGCCGCGGACGCCGCCCGCGCCGCCGAGCTCGACCCCGCCATGCCCCGGGCGCACCTCCGCAGG
GCCCACGCCTGCGTCAAGCTGGAGCAGTACGACGCCGCCCGGGCCGCCGTCGAGGCCGGCGCCGCCCTGGCCCCCAACGA
CGCGCGGTTCGCCCAGCTGATGAAGGAGATCGACTCCAAGGCGCCGAAGCCGATGGAGACCGATGCGAGCCCCGCTGCCG
CCGCCACGCCCGTGCCCGCCACCGCTCCTGCTGAAAAGCCCAAGTACAGGCACGACTACTACAACAGCGCGGCGGAGGTT
GTGGTGACCGTTTTCGCCAAGGGCGTGGCCCCCGAGCACGTCGCGGTGGAGTTCGGCGAGCAGCTGCTGAGCGTCTCCGT
CGAGGTCCCCGGCGAGGTGCCGTACCACCTGCAGCCCCGCCTGTTCGGCAAGATCATCCCCGACAAGTGCCGGTTCACCG
TCCTCTCCACCAAGATCGAGGTCCGGCTCGCTAAGGCGGAGCCGGGGACGACGTGGACGTCGCTGGAGTTCACCGACAAG
CCCAGGTTCATCGCCGCGGCGCCGCCGAGCGGGAGCAGCCCCGCCGCCGCCGGCGGCGCCCGGAGGCCGTCGTACCCGTC
GTCCAAGGGCAGGAAGGACTGGGACAAGATCGAGGCCGAGGTAAAGAAGGCGGAGAAGGACGAGAAGCTGGACGGCGACG
CGGCGGCCAACAGGTTCTTCCAGGACATCTTCAGCAACGCGGACGAGGACATGCGGCGGGCCATGACCAAGTCGTTCCAA
GAGTCCAATGGCACGGTGCTGTCCACCAACTGGAAGGACGTCGGCTCCAAGAAGATCGAGCCCAGCCCGCCGGAAGGCAT
GGATCTGCGCAAGTGGGAGTACTGA

Alignment

ORF - retro_sita_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.07 %
• Parental protein coverage: 65.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKKVEAPVAATVEDREDVANMENTQPVVEPPSKPKYRHDFYNSSTEVVLTIFAKGVPADCVVVDFGEQML
          .K..........E.....A......P...P..KPKYRHD.YNS..EVV.T.FAKGV....V.V.FGEQ.L
Retrocopy MKEIDSKAPKPMETDASPAAAATPVPATAPAEKPKYRHDYYNSAAEVVVTVFAKGVAPEHVAVEFGEQLL

Parental  SVSIEVPGEEPYHFQPRLFSKIIPEKCKYLVLSTKVEIRLAKAEQ-VTWTTLDYSGRPK---ALPQKIST
          SVS.EVPGE.PYH.QPRLF.KIIP.KC...VLSTK.E.RLAKAE...TWT.L.....P....A.P...S.
Retrocopy SVSVEVPGEVPYHLQPRLFGKIIPDKCRFTVLSTKIEVRLAKAEPGTTWTSLEFTDKPRFIAAAPPSGSS

Parental  PAET--APRPSYPSSKSKKDWDKLEAEVKKEEKDEKLDGDAALNKFFRDIYKDADEDMRRAMMKSFVESN
          PA....A.RPSYPSSK..KDWDK.EAEVKK.EKDEKLDGDAA.N.FF.DI...ADEDMRRAM.KSF.ESN
Retrocopy PAAAGGARRPSYPSSKGRKDWDKIEAEVKKAEKDEKLDGDAAANRFFQDIFSNADEDMRRAMTKSFQESN

Parental  GTVLSTNWKDVGSKKVEGSPPDGMELKKWEY
          GTVLSTNWKDVGSKK.E.SPP.GM.L.KWEY
Retrocopy GTVLSTNWKDVGSKKIEPSPPEGMDLRKWEY

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_24 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	Sb03g028430	1 retrocopy	retro_sbic_46,
Setaria italica	Si001973m.g	1 retrocopy	retro_sita_24 ,