RetrogeneDB ID: retro_sita_46

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 3:3636470..3637432(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si034718m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_46
GACAAGGATGAACAGGTTGGAGATGTCTCCAAAGCGAAAGGATGGTTCTCCTCAGTGTTCCAGAGCATTGCAGCAGGTAA
CAGTGTAATTGGCAAGTCTGATCTGCAGCCTGCGGTCAAAGCTCTGAAAGACAGGCTGATGACCAAGAACGTTGCGGAGG
AGATCGCAGAGAAGCTTTGCGAATCGATTGCAGCAAGCCTTGAGGGCAAGAAGGTAGGATCTTTCACAAGCATAGCTTCC
ACCGTCCAGGCAGCCATGGAGGAGGCTCTTCTTCGCATTCTGACCCCAAGCCGATCCATTGACATTCTGAGAGACGTGCA
CGCTGCCAAGGAGCGTGAGAGGCCGTATGTCATCGTATTCGTTGGGGTGAATGGAGTCGGCAAATCCACCAATCTTGCAA
AGGTCGCTTACTGGCTCCTCCAGCATGACCTCAGTGTGACCCTTGCAGCTTGTGATACCTTCAGGTCTGGTGCCGTTGAG
CAGCTACGCACCCATGCTCGCAGGCTCCAGATACCGATCTTTGAGAAGGGCTATGAAAGAGATCCGGCAGTCGTAGCGAA
GCAAGCGATCCAAGAAGCAACCCGGACCAAATCAGATGTTGTCCTTGTCGACACTGCTGGGCGCATGCAGGACAACGAAC
CGCTCATGAGGGCGCTCTCCAAGCTCATCAACCTCAACAGCCCGGACCTGGTCTTGTTCGTCGGGAAGCGCTGGTTGGAA
ACGACGCCGTCGATCAGCTGACCCAGTTCAACCAGAAACTGGCCGACCTGTCGCCTGTTCCAGCTGCAAGGTTGATTGAT
GGTATCCTGCTTAGCAAGTTTGACACCGTCGACGACAAGGTTGGAGCAGCGCTTTCCATGGTTTACGTTTCTGGGGCTCC
GGTTATGTTCGTGGGATGCGGTCAGTCTTACACCGACCTGAAGAAGCTGAATGTCAAGTCCATTGTTAACACCCTCCTCA
AG

Alignment

ORF - retro_sita_46 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.89 %
• Parental protein coverage: 51.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEEEEVEDGPKKKGWFSSMFQSIA-GNNVLEKADLQPALKALKDRLMTKNVAEEIAEKLCESVAASLEGK
          ...E.V.D..K.KGWFSS.FQSIA.GN.V..K.DLQPA.KALKDRLMTKNVAEEIAEKLCES.AASLEGK
Retrocopy DKDEQVGDVSKAKGWFSSVFQSIAAGNSVIGKSDLQPAVKALKDRLMTKNVAEEIAEKLCESIAASLEGK

Parental  KLGSFTRISSTVQTAMEEALVRILTPRRSIDILRDVQSAKERGRPYVIVFVGVNGVGKSTNLAKVAYWLL
          K.GSFT.I.STVQ.AMEEAL.RILTP.RSIDILRDV..AKER.RPYVIVFVGVNGVGKSTNLAKVAYWLL
Retrocopy KVGSFTSIASTVQAAMEEALLRILTPSRSIDILRDVHAAKERERPYVIVFVGVNGVGKSTNLAKVAYWLL

Parental  QHNLSVTLAACDTFRSGAVEQLRTHARRLQIPIFEKGYEKDPAVVAREAIQEASRNKSDVVLVDTAGRMQ
          QH.LSVTLAACDTFRSGAVEQLRTHARRLQIPIFEKGYE.DPAVVA..AIQEA.R.KSDVVLVDTAGRMQ
Retrocopy QHDLSVTLAACDTFRSGAVEQLRTHARRLQIPIFEKGYERDPAVVAKQAIQEATRTKSDVVLVDTAGRMQ

Parental  DNEPLMRALSKLINLNSPDLVLFVG-EALVGNDAVDQLTKFNQKLADLSAVPTARLIDGILLTKFDTIDD
          DNEPLMRALSKLINLNSPDLVLFVG.EALVGNDAVDQLT.FNQKLADLS.VP.ARLIDGILL.KFDT.DD
Retrocopy DNEPLMRALSKLINLNSPDLVLFVG<EALVGNDAVDQLTQFNQKLADLSPVPAARLIDGILLSKFDTVDD

Parental  KVGAALSMVYISGAPVMFVGCGQSYTDLKKLNVKSIVKTLLK
          KVGAALSMVY.SGAPVMFVGCGQSYTDLKKLNVKSIV.TLLK
Retrocopy KVGAALSMVYVSGAPVMFVGCGQSYTDLKKLNVKSIVNTLLK

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_46 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G78220	1 retrocopy	retro_bdis_6,
Sorghum bicolor	Sb01g050330	1 retrocopy	retro_sbic_43,
Setaria italica	Si021921m.g	1 retrocopy	retro_sita_11,
Setaria italica	Si034718m.g	1 retrocopy	retro_sita_46 ,