RetrogeneDB ID: retro_sita_51

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 4:39426374..39427124(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si035606m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_51
GCGCTGATCAACTTCGGCATCGCTTTCCTAAGAAAACAAGGCTACAAGCTCATCCAGACTCCTCTCATGATGACAAAGGA
AGCCATGGGTAAATGTGCTCAGCTATCCCAGTACGACGAGGAGCTTTACAAGCTAGAAGGAGAAGGGAAGTTTCTCATTG
CCACGTCAGAGCAGCCGCTGGCCTGTTACCATCAGGGCGAGCAGATCCATCCTGATCAGTTGCCGATCAGATACGTCGGC
TACTGAACCTGCTTCCGGAAAGAAGCTGGTTCACACGGCAGAGACACGGCCGGTATCTTCAGAACGCACGAGTTTCAGAA
GATTGAGCAATTCTGCATCACAGGCCCGGATGGCGATGAATCTTGGGAAATGCACGAGGAGATGATCAAGAATTCAGAAG
ATTTCTGCAGGGAGCTCGGCATAGCAGGCCAGATTGTCAACGTCGTGTCAGGTGCCCTTAACAATGCTGCAGCCAAGAAG
TACGATTTAGAAGGGTGGTTCCCTGCATCAAAGAACTACAGAGAACTGGTGTCATGCTCAAACTGTACGGACTATCAAGC
AAGGAGGAGGCTTGGGATCACCTATGGCCAGAGAAAGCGTGATGAACGATCAAAGAAATATGTTCACACGCTGAACTCTA
CACTGACAGCCACTGAGAGGACACTTTGCTGTATACTGGAGACGTACCAAAAGGAGGATGGTGTTGAAGTGCCCAAGCAT
ATGTATAGCAACTATCTTGCCTATCTTCCT

Alignment

ORF - retro_sita_51 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.65 %
• Parental protein coverage: 55.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALINFGLAFLRKRGFKPMQTPFFMRKETMGKCAQLAQFDEELYKVTGDGEDKYLIATSEQPLCAYHLGDR
          ALINFG.AFLRK.G.K..QTP..M.KE.MGKCAQL.Q.DEELYK..G.G..K.LIATSEQPL..YH.G..
Retrocopy ALINFGIAFLRKQGYKLIQTPLMMTKEAMGKCAQLSQYDEELYKLEGEG--KFLIATSEQPLACYHQGEQ

Parental  IYPAELPIKYAGYSTCFRKEAGSHGRDTAGIFRVHQFEKIEQFCITSPNGNDSWDIHEEMMKNSEDFYQE
          I.P..LPI.Y.GY.TCFRKEAGSHGRDTAGIFR.H.F.KIEQFCIT.P.G..SW..HEEM.KNSEDF..E
Retrocopy IHPDQLPIRYVGY*TCFRKEAGSHGRDTAGIFRTHEFQKIEQFCITGPDGDESWEMHEEMIKNSEDFCRE

Parental  IGLPYQVVSIVSGALNDAAAKKYDLEAWFPASKTFRELVSCSNCTDFQA-RRLGIGYGQKKNDEQSKQFV
          .G...Q.V..VSGALN.AAAKKYDLE.WFPASK..RELVSCSNCTD.QA.RRLGI.YGQ.K.DE.SK..V
Retrocopy LGIAGQIVNVVSGALNNAAAKKYDLEGWFPASKNYRELVSCSNCTDYQARRRLGITYGQRKRDERSKKYV

Parental  HMLNSTLTATERTLCCILENFQKEDGVEVPKALQPYMGGIEFLP
          H.LNSTLTATERTLCCILE..QKEDGVEVPK....Y......LP
Retrocopy HTLNSTLTATERTLCCILETYQKEDGVEVPKHM--YSNYLAYLP

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_51 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	Si035606m.g	1 retrocopy	retro_sita_51 ,