RetrogeneDB ID: retro_sita_25

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 4:39157722..39158799(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si006753m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si006643m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_25
ATGCTGTCGTCTTCCACCTCCCCCCTCCGCCTCCACCAACCGACCCATCCCCTCCGCCGCCACCCGCCGGCGCCGGCCGC
GGCCGCCGGCGGCGCCACCCACCTCGCCCCCTCCCGCCGGTGGCGCGGGCACCCCCGGGCGGCGCCCCTCCGGTCGCGCC
CCCAGCGCATCCGGGCGCTGGACGCCGCCCAGCCGTTCGACTACGAGTCCCGCGCGGCGGGGCTGCTGGAGGAGCGGCAG
CGGCTCAAGATCGCCATCGTCGGGTTCGGCAACTTCGGGCAGTTCCTGGCGCGCACCTTCGCGCGGCAGGGCCACACGCT
GCTCGCCCACTCCCGGACCGATCACTCGGCGCTCGCCGCCACGCTGGGCGCCTCCTTCTTCACCGACCCGCACGACCTCT
GCGAGTGCCACCCGGACGTGGTGCTCCTCGCCACCTCCATCCTCTCCGCCGAGGCCGTCCTCCGCTCGCTCCCCGTCCAC
CGCCTCCGCCGCAACACCCTCTTCGTCGACGTGCTCTCCGTCAAGGAGTTCCCCAAGAACCTCCTCCTCAGCTCCCTCCC
CCCCGACTTCGACGTCATCTGCACCCACCCCATGTTCGGCCCGGAGTCCGCGCGCGACGGCTGGGACGGCCTCCCCTTCG
TCTTCGACAAGGTCCGCGTCGGCGACTGCCCCGCCCGCCGCGCCCGCGCCGAGGCCTTCCTCAACATCTTCGAGCGCGAG
GGATGCCGGATGGTCGAAATGTCCTGCGCCGAGCACGACGCGCACGCCGCCGAGACCCAGTTCCTCACCCACTCCGTCGG
CCGGATGCTCGCCATGCTCGAGCTCCGCTCCACGCCCATCAACACCAAGGGCTACGAGACGCTGCTCCGGCTCGTCGACA
ACACCTGCAGCGACAGCTTCGACCTCTACAATGGCCTCTTCATGTACAACAAGAACTCCACCGAGCTGCTCAACCGCCTC
GAATGGGCCATGGACTCCGTCAAGAAGAAGCTCTTCGACGGCCTGCACGACGTGCTCCGGAAGCAGCTCTTCGAGGGCAC
GGCGCCGGCCCCAAACACCACCAACGTCCGCAAGTAA

Alignment

ORF - retro_sita_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.09 %
• Parental protein coverage: 68.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRVGIVGFGNFGQFIAGGIQRQGHAVLAASRSDYSAYCADHGIRFFGSVDALCEERPDVLLICSSILSTE
          L...IVGFGNFGQF.A....RQGH..LA.SR.D.SA..A..G..FF.....LCE..PDV.L...SILS.E
Retrocopy LKIAIVGFGNFGQFLARTFARQGHTLLAHSRTDHSALAATLGASFFTDPHDLCECHPDVVLLATSILSAE

Parental  SVVSAIPFHKLRPDTIVADVLSVKQFPRNLLLEILPPGFGIVCTHPMFGPESGKHGWGKLPFVYNKVRVA
          .V....P.H.LR..T...DVLSVK.FP.NLLL..LPP.F...CTHPMFGPES...GW..LPFV..KVRV.
Retrocopy AVLRSLPVHRLRRNTLFVDVLSVKEFPKNLLLSSLPPDFDVICTHPMFGPESARDGWDGLPFVFDKVRVG

Parental  EGGDQATKCDQFLSIFEQEGCRMVEMSCAEHDRYAAGSQFITHTIGRVLSQLNLKSTPINTKGYESLLQL
          ...........FL.IFE.EGCRMVEMSCAEHD..AA..QF.TH..GR.L..L.L.STPINTKGYE.LL.L
Retrocopy DCPARRARAEAFLNIFEREGCRMVEMSCAEHDAHAAETQFLTHSVGRMLAMLELRSTPINTKGYETLLRL

Parental  THNTVSDSFDLYYGLFMYNVNATEQLDNLERAFEKVRQMLYGRLHDLLRKQIVE
          ..NT.SDSFDLY.GLFMYN.N.TE.L..LE.A...V...L...LHD.LRKQ..E
Retrocopy VDNTCSDSFDLYNGLFMYNKNSTELLNRLEWAMDSVKKKLFDGLHDVLRKQLFE

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_25 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB06G25340	1 retrocopy	retro_obra_15,
Oryza rufipogon	ORUFI06G18690	1 retrocopy	retro_oruf_8,
Setaria italica	Si006643m.g	1 retrocopy	retro_sita_25 ,