RetrogeneDB ID: retro_sita_12

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 7:1255865..1257257(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si011729m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si011975m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_12
ATGGAGTCATTCCTAAAGAAGTTCTTCCCGGAGGTGCTGCGTGGGATGAAGAGCGCAAAGCGCGACGCCTACTGCAAGTA
TGACAACCATCTTCTTACCGCGTTCACGTCATCGCTGTACATCGCAGCCACTCTGGCATCACTGGTGGCGAGCCGTGTGA
CGAGAAGGGTAGGTCGCCAAGCCATCATGCTCATCGGTGGCGCCTTGTTCCTCGCCGGCTCCATCATCAACGCTGCGGCC
GTCAACGTTGCCATGCTCATCATCGGCCGGATTCTGCTAGGCTTTGGTGTCGGCTTCACAGCACAGGCGGCTCCCCTGTA
TCTCGCCGAGACATCCCCTGCAAGGTGGCGCGGAGCGTTCACCATGGCCTACCACAGCTTCCTCTGCGCCGGCACAGTGA
TCGCAAACGTCGTCAACTACTTGACAAACCCCATCCCGGACTGGGGCTGGCGCGTCTCGCTCGGCGCCGCGGCGGTGCCA
GCCATCGTCATCGTCGCCGGCGCCCTCTTGGTCCCGGACACCCCCAGCAGCCTCGTGCTTCGCGGTCAGCAGGACAGGGC
CCGCGCGTCGCTGCAGCGCATCCGCGGCGCGGACGCCGACGTCGAGGCCGAGTTCAAGGACATAGTCTGCGCCGTCGAGG
AGGCGCGCCGGCACGACGAGGGCGCGCTGAAGAGGCTGCGCAGCAAGGGGTACCGGCCCTACGCGGTGATGATGGTGGCC
ATACCCGTGTTCTTCGAGTTCACGGGCTTCATCGTCATCTTCATCTTCGCGCCGGTGCTGTTCCGGACGGTCGGGTTCAG
CAGCCAGAAGGCCATCCTGGGCTCCGTCATCATCAACCTCGTGGGCTTGTGCGCTGTCGTCATGTCCTCCTTGGTCGTCG
ACCGCTTCGGCCGCAGGTTCTTGTTCCTCGCCGGCGGCGTCAGCATGCTGCTCTGCCAGGTGGCCGTGTCATGGATCCTA
GCAGCGCACCTCGGGAAGCACGACGCCGCAGCGGGGGTGACGATGGCGCGGAGCTACGCGGAGGCGGTGCTCGTGCTCAT
GTGCCTCTACACCTTCAGCATGGGCTTCTCCTGGGGTCCGGTGAAGTGGGTGATATGGAGCGAGATCCACCCGGTGGACG
TGAGGTCCGTGGGGCAGGCCATCTCCCTGTCCATCGCCTTCGTCATCTCCTTCGTGGAGACGCAGGTGTTCATGTCCCTG
CTCTGCAGCCTCAAGTTCGCGATATTCCTCTTCTTCGCAGGATGGGTCCTGGCGATGACGGCTTTCATCGCGGCGTTCCT
GCCGGAGACCAAGGGCGTGCCGCTCGAGGCCATGCGAGCGGTATGGGCACGTCATTGGTACTGGAGGAGGTTTGTCGTCG
TACAGGACGCTAATAAGATTCCAGTTGAGTAA

Alignment

ORF - retro_sita_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.13 %
• Parental protein coverage: 89.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESFLNKFFPEVLRGMRSAKRDAYCKYDNQLLTAFTSSMYIAGMLASLVASGVTRRAGRKAVMLAGGTMF
          MESFL.KFFPEVLRGM.SAKRDAYCKYDN.LLTAFTSS.YIA..LASLVAS.VTRR.GR.A.ML.GG..F
Retrocopy MESFLKKFFPEVLRGMKSAKRDAYCKYDNHLLTAFTSSLYIAATLASLVASRVTRRVGRQAIMLIGGALF

Parental  LAGSVINAGAVNIAMLIIGRILLGFGVGFTAQAAPLYLAETSPTRWRGAFTSAYHIFLVAGTLAANVANY
          LAGS.INA.AVN.AMLIIGRILLGFGVGFTAQAAPLYLAETSP.RWRGAFT.AYH.FL.AGT..ANV.NY
Retrocopy LAGSIINAAAVNVAMLIIGRILLGFGVGFTAQAAPLYLAETSPARWRGAFTMAYHSFLCAGTVIANVVNY

Parental  FTNRIPGWGWRVSLGLAAVPATVIVLGALFVSDSPSSLLLRGEPEKARESLQRVRGPDAHVEAEFKDIAR
          .TN.IP.WGWRVSLG.AAVPA.VIV.GAL.V.D.PSSL.LRG....AR.SLQR.RG.DA.VEAEFKDI..
Retrocopy LTNPIPDWGWRVSLGAAAVPAIVIVAGALLVPDTPSSLVLRGQQDRARASLQRIRGADADVEAEFKDIVC

Parental  AVEEARRNEEGAFRRLRGKGYRHYLVMAVAIPTFFDLTGMIVITVFSPVLFRTVGFDSQKAVFGAVIISL
          AVEEARR..EGA..RLR.KGYR.Y.VM.VAIP.FF..TG.IVI..F.PVLFRTVGF.SQKA..G.VII.L
Retrocopy AVEEARRHDEGALKRLRSKGYRPYAVMMVAIPVFFEFTGFIVIFIFAPVLFRTVGFSSQKAILGSVIINL

Parental  VSLSGVVLSTVVVDRCGRRFLFLAGGTAMLIFQVAVSWILADHLGKHGAA---TMPRNYAVGVVVLMCLY
          V.L..VV.S..VVDR.GRRFLFLAGG..ML..QVAVSWILA.HLGKH.AA...TM.R.YA..V.VLMCLY
Retrocopy VGLCAVVMSSLVVDRFGRRFLFLAGGVSMLLCQVAVSWILAAHLGKHDAAAGVTMARSYAEAVLVLMCLY

Parental  TFSFSLSWGPLKWVVPSEIYPVDIRSAGQAVTLSVALTLSFTQTQVFISMLCAMKYAIFLFYSGWVLAMT
          TFS...SWGP.KWV..SEI.PVD.RS.GQA..LS.A...SF..TQVF.S.LC..K.AIFLF..GWVLAMT
Retrocopy TFSMGFSWGPVKWVIWSEIHPVDVRSVGQAISLSIAFVISFVETQVFMSLLCSLKFAIFLFFAGWVLAMT

Parental  VFIAAFLPETKGVPLEAMRSVWAGHWFWRRFVVLDAKQEV
          .FIAAFLPETKGVPLEAMR.VWA.HW.WRRFVV.......
Retrocopy AFIAAFLPETKGVPLEAMRAVWARHWYWRRFVVVQDANKI

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_12 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	Si011975m.g	1 retrocopy	retro_sita_12 ,