RetrogeneDB ID: retro_sita_31

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 6:35753524..35754370(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si015425m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si037085m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_31
ATGGCACCACCGCCGGCGACGTCGAGAAGAGGTCCTCTCGTCGTGCCGCTGCTGCTGCTGCTGGCGGCGCTCGACGTCGC
AGGTGCGAGCGGCCACAAGCCCTTGACGCCCGGCGGGCGCCTGGTGCACCACAACCACGGCAAGTTCACGGCCGGCCCCT
GGAAGCCCGCGCACGCCACCTTCTACGGCGGGCGCGACGGCTCCGACACGACGGCGGGCGCGTGCGGGTACAAGGACACG
CGGGCGGAGGGGTACGGCGTGCAGACGGTGGCGGTGAGCACGGTGCTGTTCGGCGACGGCGCGGCGTGCGGCGGATGCTA
CGAGGTGCGGTGCGTGGACAGCCCCCACGGCTGCAAGGCGGCGGCGGCGGCGCCGCTGGTGGTGACGGCGACGAACCTGT
GCCCGCCCAACTACCAGCAGTCGAGCGACAACGGCGGGTGGTGCAACCCGCCGCGGGAGCACTTCGACCTGAGCATGCCG
GCGTTCCTGCAGATCGCGGAGGAGAAGGCCGGGATCGTGCCCATCTCCTACCGGCGGGTGGCGTGCGTGAAGCAGGGCGG
CATCCGCTACACCATCACCGGGAACAGGTACTTCAACATGGTGATGGTGACCAACGTGGGCGGCGCCGGCGACCTGGCGG
CGGTGTCGGTGAAGGGGAGCAAGCGCGTCAAGTGGACGGAGCTGAAGCGCAACTGGGGGCAGGTGTGGCAGACCGGGGAA
GACCTCACCGGAGAGTCGCTGACGTTCCGGCTGATGACCAGCGACCACCGCAAGGCCACATCCTGGCACGTCCTCCCCAC
CAACTGGCAGTTCGGCGTCACCTACGAGGCGACCAAGAACTTCTAG

Alignment

ORF - retro_sita_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.36 %
• Parental protein coverage: 89.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVYGGGAWQSAHATFYGGSDASGTMGGACGYGNLYSQGYGVNNAALSTALFNEGQSCGACFEIKCENQPG
          G....G.W..AHATFYGG.D.S.T..GACGY......GYGV...A.ST.LF..G..CG.C.E..C...P.
Retrocopy GKFTAGPWKPAHATFYGGRDGSDTTAGACGYKDTRAEGYGVQTVAVSTVLFGDGAACGGCYEVRCVDSPH

Parental  WRWCHPGSPSILVTATNFCPPNYALPSDDGGWCNPPRPHFDLAMPMFLHIAEYRAGIVPVSYRRVPCRKS
          ........P...VTATN.CPPNY...SD.GGWCNPPR.HFDL.MP.FL.IAE..AGIVP.SYRRV.C.K.
Retrocopy GCKAAAAAP-LVVTATNLCPPNYQQSSDNGGWCNPPREHFDLSMPAFLQIAEEKAGIVPISYRRVACVKQ

Parental  GGIRFTINGFRYFNLVLITNVAGAGDIVRASVKGS-GTGWLPMSRNWGQNWQSNAILVGDALSFRVTGSD
          GGIR.TI.G.RYFN.V..TNV.GAGD....SVKGS....W....RNWGQ.WQ....L.G..L.FR...SD
Retrocopy GGIRYTITGNRYFNMVMVTNVGGAGDLAAVSVKGSKRVKWTELKRNWGQVWQTGEDLTGESLTFRLMTSD

Parental  RRTSTSWNAAPRNWQFGQTFEG-KNF
          .R..TSW...P.NWQFG.T.E..KNF
Retrocopy HRKATSWHVLPTNWQFGVTYEATKNF

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_31 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Setaria italica	Si037085m.g	1 retrocopy	retro_sita_31 ,