RetrogeneDB ID: retro_sita_16

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 1:3969906..3971235(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si019049m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si008152m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_16
ATGGCAGCTGCCACAGCCGTGTTCGCCGCAACCAGCGCCAGAGCCACCGCTCCTCTCCTTCACCGCAGCCGGACCCGGAA
CTACTCGTGCGGCCTTGCGACTGCGGGGCCGTCGCCGTCGCCGTCGTCGTGTGCCAGTGCCAATGTCCGCCGGCGCCGCC
CGATACCGGCGTCGTCTTGCGGCGTCCATGGACGCGGCCCCCTCGTCCCCGCGTCCGACCACTGGGGCAACTGGACCTTC
CTCCTGACCACCGCCGCGCTGGGCATCTGGTCGGAGAAGCGGACCCCGGTGGGGAAGGCGCTTAGCGGGGCGCTGGTGAG
CGTGCTGCTGGGTCTCGCGGCCAGCAGCGCCGGCGTGGTGGCGGCGGACGCCCCGGCGTACCGCGTGGTGCTCGACTACC
TCCTGCCGCTCGCCATCCCGCTGCTGCTCTTCCGCGCCGACCTCCGCCGCGTGCTCCGCTCCACCGGCGCGCTGCTGCTG
GCCTTCCTGCTCGGGTCCGCGGCGACGGCGGCGGGTACGGTGGTGGCGTTCCTCCTCGTCCCGATGCGGTCGCTGGGCCC
GGACAACTGGAAGATCGCGGCGGCGCTGATGAGCCGCCACATCGGGGGCGCCGTCAACTACGTTGCCGTCTCCGAAGCTC
TCGGGGTCTCCCCGTCGGTGCTGGCGGCCGGGCTCGCCGCCGACAACATCATCTGCGCGCTCTACTTCACGAGCCTCTTC
GCACTGGCCGCCAAGATCCCCAAGGAAGACCCAACGGGGAGCGACGGCGAGTCCGTGGCCGGCGACGACAGCAGCAGCAG
CAGCAGCAGCAGCCACAGCGCCGTGGCCATGGCGGCCGCGTTCGCCATATGTAAGGCGGGGAAGCTGGCGGCGGCCGCGC
TGGGCATACAAGGGGGAAGCCTCCCCTGCATAACAGTGGTCTCGGTGGCTCTGGCGACGCTGTTCCCCTCGCAGATCGGG
AAGCTGGCGCCGTCGGGCGAGGCCATGGCCGTGGTCCTGATGCAGGTGTTCTTCGCCGTAGTGGGAACCAACGGAAGCGT
CGGCAACGTCCTCGACACGACGCCTGCCATATTCGCCTTCGCCTTCGTGCAAATCGCCGTGCACCTCCTGCTGACCCTGG
GCGTCGGCAAGCTGCTCGGCATCGACCGCAAGCTGCTGCTGATCGCGTCCAACGCCAACGTGGGCGGCCCGACCACCGCC
TGCGGGATGGCCACCGCCAAGGGGTGGTCCTCTCTGGTGGTTCCGGGGATCCTCGCCGGCATCTTGGGCATCGCCATCGC
CACCTTCGCGGGAATCGCCTTCGGCGTGCTCGTCCTCAAACGCATGTAG

Alignment

ORF - retro_sita_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.23 %
• Parental protein coverage: 84.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAIAAGDHWGNWAFLLSAAAFGTWSEEKTSWGAALSGALVSILAGLAATAAGLISPGAPAHGAVMEYLLP
          P...A.DHWGNW.FLL..AA.G.WSE..T..G.ALSGALVS.L.GLAA..AG.....APA...V..YLLP
Retrocopy PLVPASDHWGNWTFLLTTAALGIWSEKRTPVGKALSGALVSVLLGLAASSAGVVAADAPAYRVVLDYLLP

Parental  AAVPLLLLGADLRRVVRTTGDLLKAFLIGSVATIIGTTVAYLLVPMRSLGHDSWKIAAALMGSYIGGAVN
          .A.PLLL..ADLRRV.R.TG.LL.AFL.GS.AT..GT.VA.LLVPMRSLG.D.WKIAAALM...IGGAVN
Retrocopy LAIPLLLFRADLRRVLRSTGALLLAFLLGSAATAAGTVVAFLLVPMRSLGPDNWKIAAALMSRHIGGAVN

Parental  FVAVSEALGITPSVVAAGVAADNLISALYFMILFSLASKIPAEPKNAATDGRKDGGEPEGDGRFSVLNGG
          .VAVSEALG..PSV.AAG.AADN.I.ALYF..LF.LA.KIP.E......DG....G........S.....
Retrocopy YVAVSEALGVSPSVLAAGLAADNIICALYFTSLFALAAKIPKEDP-TGSDGESVAGD-DSSSSSSSSHSA

Parental  AAIALSFVICKAGSAIADRLGFQGGTLPCVTALVVFLATAFPGQLGKLAPAGETMALILMQLFFTVVGAN
          .A.A..F.ICKAG...A..LG.QGG.LPC.T...V.LAT.FP.Q.GKLAP.GE.MA..LMQ.FF.VVG.N
Retrocopy VAMAAAFAICKAGKLAAAALGIQGGSLPCITVVSVALATLFPSQIGKLAPSGEAMAVVLMQVFFAVVGTN

Parental  GNVVDAVTKAPSVFAFALVQVSVHLAVLLGVGKLVGLDRKPLLIASNANIGGPTTAAAMATAKGWSSLIV
          G.V.......P..FAFA.VQ..VHL...LGVGKL.G.DRK.LLIASNAN.GGPTTA..MATAKGWSSL.V
Retrocopy GSVGNVLDTTPAIFAFAFVQIAVHLLLTLGVGKLLGIDRKLLLIASNANVGGPTTACGMATAKGWSSLVV

Parental  PGILVGIFGISIATFLGIGFGMLVLRRM
          PGIL.GI.GI.IATF.GI.FG.LVL.RM
Retrocopy PGILAGILGIAIATFAGIAFGVLVLKRM

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_16 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Setaria italica	Si008152m.g	1 retrocopy	retro_sita_16 ,