RetrogeneDB ID: retro_sita_37

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 1:8719125..8720496(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si019748m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si024807m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_37
ATGGCGGCGTTGTCGGCGCCGGACCTGTTGGAGGAGTACGTGGAGAAGGTGGAGGAGCGGAAGCAGGAGGAGCGGCTCCG
CGACGCGCGCCTCGACGACTGGCTCCCCATCACCTCCTCCCGCACGGCCAAGTGGTACTACTCGGCCTTCCACAACGTGA
CGGCCATGGTGGGCGCCGGAGTTCTGGGGCTCCCCTTCGCCATGTCGCAGCTCGGGTGGTCCGCCGGGACGGTCGCCATC
GTGGGCTCCTTCGGCGTCACGCTCTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTCCCCGGCAAGCGCTTCGA
CCGGTACCACGAGCTCGGGCAGCACGCGTTCGGGAAGCGCCTCGGGCTCTGGATCATCGTGCCGCAGCAGCTCATCGTCG
AGGTCGGCACCGACGTCGTCTACATGGTCACCGGCGGCCAGTCGCTCAAGAAGGTGTACGACCTCGTCTGCGCCGGCCGG
TGCAAGGACATCCGCCTCGCCTTCTGGATCATGGCGTTCGCCGCCGTCCAGCTCCCGCTCTCGCAGTTCCCAAACTTCAA
CTCCATCTCCGCCGTCTCCGCCGCCGCCGCTCTCATGTCGCTCACCTACTCCATGATCGCCTTCTTCGCCTCCGCCTTCA
AGGGCGCCCACGCCGGCGCTGCCGCCGACTACGCGCTCAGGGCGCCCACCACCGCCGGCAAGGTGTTCGGCGTGCTCAAC
GCGCTCGGCGCCGTCGCGTTCGCCTACGCAGGCCACAACGTCGTGCTGGAGATCCAGGCCACGATCCCGTCCACGCCGGA
GAAGCCGTCGAAGAAGCCCATGTGGCGCGGGGTCATCGTCGCATACGCCATCGTCGGGCTCTGCTACTTCGCCGTCGCCT
TCGCCGGCTACTACGCCTTCGGCAACACCGTCGACCCCAACGTGCTCATCTCCCTCGAGAAGCCGCGGTGGCTCGTCGCG
GCGGCGAACCTCATGGTTGCCGTCCACGTCGTCGGCAGCTACCAGGTGTTCGCCATGCCAGTGTTCGACATGATGGAGAC
GGTGCTGGTGAAGAAGCACCGGTTCACGCCGGGGATCGGGCTTCGCCTCGTCGCGCGCTCCGCCTACGTCCTCGCCACCA
TGTTCGTCGGCATGACCTTTCCCTTCTTCGACGGCCTGCTGGGGTTCTTCGGTGGGTTCGGATTCGCGCCGACGACATAC
TTCATCCCCTGCATCATCTGGCTGATGCTCAAGAAGCCCAAGAAGTACGGGTTCACATGGTTCTTCAACATCTTCTGCAT
CCTGATCGGGGTGCTCTTGATGATCGCCTCCCCCATCGGAGGCATGAGGCAGATCATCCATGACGTAAATAGCTTCAAGT
TCTACAGTTAG

Alignment

ORF - retro_sita_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDQYVETAKERRQEERLKNVNLDDWLPITSSRTAKWYYSAFHNVTAMVGAGVLGLPFAMSQLGWGLGTVV
          ...YVE...ER.QEERL....LDDWLPITSSRTAKWYYSAFHNVTAMVGAGVLGLPFAMSQLGW..GTV.
Retrocopy LEEYVEKVEERKQEERLRDARLDDWLPITSSRTAKWYYSAFHNVTAMVGAGVLGLPFAMSQLGWSAGTVA

Parental  IVMSFVITLYTLWQMVEMHEMVPGKRFDRYHELGQHAFGKRLGLWIIVPQQLIVEVGTDIVYMVTGGQCL
          IV.SF..TLYTLWQMVEMHEMVPGKRFDRYHELGQHAFGKRLGLWIIVPQQLIVEVGTD.VYMVTGGQ.L
Retrocopy IVGSFGVTLYTLWQMVEMHEMVPGKRFDRYHELGQHAFGKRLGLWIIVPQQLIVEVGTDVVYMVTGGQSL

Parental  RKFHDLVCQGRSCADIRLTYWIMIFGSVHFPLSQFPNFNSISAVSAAAAVMSLTYSMIAFFASTVKGAST
          .K..DLVC.GR.C.DIRL..WIM.F..V..PLSQFPNFNSISAVSAAAA.MSLTYSMIAFFAS..KGA..
Retrocopy KKVYDLVCAGR-CKDIRLAFWIMAFAAVQLPLSQFPNFNSISAVSAAAALMSLTYSMIAFFASAFKGAHA

Parental  AAAVDYGLRASTATGRVFGVLNALGAVAFAYAGHNVVLEIQATIPSTPETPSKRPMWRGVVVAYAIVALC
          .AA.DY.LRA.T..G.VFGVLNALGAVAFAYAGHNVVLEIQATIPSTPE.PSK.PMWRGV.VAYAIV.LC
Retrocopy GAAADYALRAPTTAGKVFGVLNALGAVAFAYAGHNVVLEIQATIPSTPEKPSKKPMWRGVIVAYAIVGLC

Parental  YFCVAFGGYYAFGNAVEPNVLISLERPRWLIAAANLMVVVHVVGSYQVYAMPVFDMIETVLVKKHRFTPG
          YF.VAF.GYYAFGN.V.PNVLISLE.PRWL.AAANLMV.VHVVGSYQV.AMPVFDM.ETVLVKKHRFTPG
Retrocopy YFAVAFAGYYAFGNTVDPNVLISLEKPRWLVAAANLMVAVHVVGSYQVFAMPVFDMMETVLVKKHRFTPG

Parental  VRLRLIARSAYVAATMFIGMTFPFFDGLLGFFGGFGFAPTTYYIPCIIWLMLRKPKKYGLSWTINIMCIV
          ..LRL.ARSAYV.ATMF.GMTFPFFDGLLGFFGGFGFAPTTY.IPCIIWLML.KPKKYG..W..NI.CI.
Retrocopy IGLRLVARSAYVLATMFVGMTFPFFDGLLGFFGGFGFAPTTYFIPCIIWLMLKKPKKYGFTWFFNIFCIL

Parental  IGVILTLISPIGGMRQIILDAKNFKLYS
          IGV.L...SPIGGMRQII.D...FK.YS
Retrocopy IGVLLMIASPIGGMRQIIHDVNSFKFYS

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_37 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	Si024807m.g	1 retrocopy	retro_sita_37 ,