RetrogeneDB ID: retro_sita_29

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 9:269527..270649(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si036235m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si001573m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_29
ATGGTGCAGGCTGCGCTTGATGACACCAAGCAGCAGCAGCAGCAGCCTCCTCTTGTGTTCGACGCCGCCCGGCTGAGCGG
CCAGGCCGACATCCCCGAGCAGTTTTTGTGGCCGGCGGACGAGAGCCCCACCCCGGACGCCGTCGAGGAGCTGCCCGTGC
CTCTCATCGACCTCTCCGGCGGCGCCGCCAACGCCGAGGTGGTGCGCCAGGTGGGCGACGCCTGCGGGCTCCACGGCTTC
TTCCAGGTGGTGAACCACGGCATCGACCCGGCGCTGCTCGCCGAGGCCCACCGCTGCATGGACACCTTCTTCACGCTGCC
CCTCGCCGACAAGCAGCGCGCGCAGCGCCGCCCGGGCGAGAGCTGCGGCTACGCCAGCAGCTTCACGGGGCGGTTCGCCT
CCAAGCTGCCATGGAAGGAGACGCTGTCGTTCCGCTACTCTCCTTCCGACGACGTCGCCGGCGAGCAGCTCGTCAGCAGC
TACTTCGTGGAGAAGCTGGGCGAGGCGTATCGCCACCACGGCGAGGTGTACGGTCGCTACTGCTCGGAGATGAGCCGGCT
GTCGCTGGAGATCATGGAGGTGCTGGGGGAGAGCCTGGGCGTGGGGCCCTCCCACTTCCGGCGATTCTTCGAGGGTAACG
ACTCCATCATGCGCCTCAACTACTATCCGCCATGCCAGCGGCCCTACGACACGCTCGGCACCGGGCCGCATTGCGACCCC
ACCTCCCTCACCATCCTCCACCAGGACGACGTCGGCGGCCTCCAGGTCTTCGCCGGCGGGCGGTGGCGCTCCATCCGCCC
CCACGCCGGAGCCTTCGTCGTCAACATCGGCGACACCTTCATGGCGCTCTCCAACGGCCGGTACCGGAGCTGCCTCCACC
GCGCCGTCGTCAACAGCCGCGTGCCGCGCCGCTCGCTCGCCTTCTTCCTCTGCCCGGAGATGGACAAGGTGGTGCGGCCG
CCGGGGGAGCTCGTCGACGACCGCAACCCGAGGGCGTACCCGGACTTCACGTGGCGGGCGCTGCTGGACTTCACCATGAG
GCACTACAGGGCGGACATGAGGACGCTCGAGGCATTCTCAAACTGGCTCCTCATCCATGGCAACAACAGCCACCAACTCT
GA

Alignment

ORF - retro_sita_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.22 %
• Parental protein coverage: 68.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVAAACATHGFFQVCGHGVGADLARAALDGASDFFRLPLAEKQRARRVPGTVSGYTSAHADRFASKLPWK
          QV..AC..HGFFQV..HG....L...A......FF.LPLA.KQRA.R.PG...GY.S....RFASKLPWK
Retrocopy QVGDACGLHGFFQVVNHGIDPALLAEAHRCMDTFFTLPLADKQRAQRRPGESCGYASSFTGRFASKLPWK

Parental  ETLSFGFH---DGAASPVVVDYFAGTLGQDFEAVGRVYQRYCEEMKALSLTIMELLELSLGVERGYYRDF
          ETLSF......D.A....V..YF...LG......G.VY.RYC.EM..LSL.IME.L..SLGV.....R.F
Retrocopy ETLSFRYSPSDDVAGEQLVSSYFVEKLGEAYRHHGEVYGRYCSEMSRLSLEIMEVLGESLGVGPSHFRRF

Parental  FEDSRSIMRCNYYPPCPEPERTLGTGPHCDPTALTILLQDDVGGLEVLVDGDWRPVRPVPGAMVINIGDT
          FE...SIMR.NYYPPC..P..TLGTGPHCDPT.LTIL.QDDVGGL.V...G.WR..RP..GA.V.NIGDT
Retrocopy FEGNDSIMRLNYYPPCQRPYDTLGTGPHCDPTSLTILHQDDVGGLQVFAGGRWRSIRPHAGAFVVNIGDT

Parental  FMALSNGRYKSCLHRAVVNQRQERRSLAFFLCPREDRVVRPPASGAVGEAPRRYPDFTWADLMRFTQRHY
          FMALSNGRY.SCLHRAVVN.R..RRSLAFFLCP..D.VVRPP........PR.YPDFTW..L..FT.RHY
Retrocopy FMALSNGRYRSCLHRAVVNSRVPRRSLAFFLCPEMDKVVRPPGELVDDRNPRAYPDFTWRALLDFTMRHY

Parental  RADTRTLDAFTRWL
          RAD.RTL.AF..WL
Retrocopy RADMRTLEAFSNWL

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_29 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR01G34060	1 retrocopy	retro_lper_3,
Oryza barthii	OBART01G39570	1 retrocopy	retro_obar_12,
Oryza meridionalis	OMERI01G36440	1 retrocopy	retro_omer_11,
Oryza glaberrima	ORGLA01G0334700	1 retrocopy	retro_ogla_32,
Oryza sativa japonica	OS01G0883800	1 retrocopy	retro_osat_2,
Setaria italica	Si001573m.g	1 retrocopy	retro_sita_29 ,
Setaria italica	Si012266m.g	1 retrocopy	retro_sita_32,