RetrogeneDB ID: retro_sita_5

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 4:28050021..28051053(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si006817m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si020002m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_5
ATGGAGATGAGCCGCGCGGCTCTGGACGACGTGATCCGGCGGCTCCTGGACGCGCGGCGGTGGCGCCCGGCGGGGAAGCA
GCAGCAGCAGCTGCTGGCGGAGGGGGAGATCCGGCAGCTCTGCGCCGGCGCCAAGGCCGTGTTCCTGCGGCAGCCAAACC
TCCTGGAGCTGGACGCGCCCATCAACGTCTGCGGCGACGTGCACGGCCAGTTCCGCGACCTCGTCCGGATCCTGCAGGAG
CTTGGCGGCCTCCCGCCGCGGAGCAAGTACCTGTTCCTGGGCGACTACGTGGACCGCGGCGACCAAAGCCTGGAGACCAT
CTGCCTGCTGCTGGCCTACAAGGTCCGGTACCCGGAGCATGTGTTCCTCCTCCGCGGCAACCACGAGTGCGCCTCCATCA
ACCGCATCTACGGCTTCTACGACGAGTGCAAGCGCCGCTACACCGTCCGCCTCTGGCGCACCTTCACCGACTGCTTCAAC
TGCCTCCCCGCCGCCGCGCTCGTCGACGACCGCATCCTCTGCGTCCACGGCGGCATCTCGCCGCACCTCCGCAGCCTCGA
CCAGATCCGGGACCTGCCCAGGCCCTGCGACGTCCCAGACGAGGGCCTGCTCTGCGACCTGCTCTGGTCGGACCCGGCCG
CCGGCGTCCGGGGCTGGGCGCCCAACGACGACAGGGGCGTCTCATGCACCTTCGGCGCCGACGTGCTCAAGGCCTTCCTC
CGCACCCACGACCTAGACCTCCTCTGCAGGGCGCACCAGGTGGTCGAGGACGGATACGAGTTCTTCGCAGACCGCCAACT
CGTCACCGTCTTCTCCGCGCCAAACTACTGCGGCGAATTCGACAACGCCGGCGCCATCATGTCCATCGACGCGGACCTCG
TATGCTCCTTCCACATCATCAAGCCGGCGGCGGGCGACACAACCACCAACAGGGGCATCGCCGCCGCCTGGGGCCGCAGC
AGCGCCGCCTCAGCGTCGTCGTCCTCGTCTTCCGGCAGAAGCACAAAAAAGGGGTTGATGCGCTACTGGTAG

Alignment

ORF - retro_sita_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.78 %
• Parental protein coverage: 80.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EMDPALLDDVIRRLLEVKNLKP-GKNAQ--LSESEIKQLCAAAKEIFLQQPNLLELEAPIKICGDVHGQF
          EM..A.LDDVIRRLL......P.GK..Q..L.E.EI.QLCA.AK..FL.QPNLLEL.API..CGDVHGQF
Retrocopy EMSRAALDDVIRRLLDARRWRPAGKQQQQLLAEGEIRQLCAGAKAVFLRQPNLLELDAPINVCGDVHGQF

Parental  SDLLRLF-DYGGYPPQSNYLFLGDYVDRGKQSLETICLLLAYKVKYPENFFLLRGNHECASVNRIYGFYD
          .DL.R.....GG.PP.S.YLFLGDYVDRG.QSLETICLLLAYKV.YPE..FLLRGNHECAS.NRIYGFYD
Retrocopy RDLVRILQELGGLPPRSKYLFLGDYVDRGDQSLETICLLLAYKVRYPEHVFLLRGNHECASINRIYGFYD

Parental  ECKRRFSVKLWKTFTDCFNCLPVSALIDEKILCMHGGLSPELNKLDQILNLNRPTDVPDTGLLCDLLWSD
          ECKRR..V.LW.TFTDCFNCLP..AL.D..ILC.HGG.SP.L..LDQI..L.RP.DVPD.GLLCDLLWSD
Retrocopy ECKRRYTVRLWRTFTDCFNCLPAAALVDDRILCVHGGISPHLRSLDQIRDLPRPCDVPDEGLLCDLLWSD

Parental  PSNEAQGWAMN-DRGVSYTFGPDKVAEFLEKHDLDLICRAHQVVEDGYEFFANRQLVTIFSAPNYCGEFD
          P.....GWA.N.DRGVS.TFG.D....FL..HDLDL.CRAHQVVEDGYEFFA.RQLVT.FSAPNYCGEFD
Retrocopy PAAGVRGWAPNDDRGVSCTFGADVLKAFLRTHDLDLLCRAHQVVEDGYEFFADRQLVTVFSAPNYCGEFD

Parental  NAGAMMSVDETLMCSFQILKPARKMLAGSTNNKSGFKSLRG
          NAGA.MS.D..L.CSF.I.KPA....AG.T....G.....G
Retrocopy NAGAIMSIDADLVCSFHIIKPA----AGDTTTNRGIAAAWG

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_5 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	Si020002m.g	1 retrocopy	retro_sita_5 ,