RetrogeneDB ID: retro_sita_3

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 9:5156387..5157761(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si040038m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si035607m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_3
ATGGCGGCAACTCGCGTCCTGGTGCTGCCTTACCCCGCGCAGGGCCATGTCATCCCTATGATGGAGCTCTCCCACAGCCT
CGTCGAGCACGGTGTCAAGGGCACCTTCGTCAACACCGAGCTGAACCACGGCCTCATCCTTGGCGCCTTGGCGAGCAGGG
ACAGCGTGCTCGGCGGTGTCGACATGGTGTCGGTGCCCGACGGCCTGGGCTGCGGCGAAGACCGGAAGGACCTCGCCCGT
CTCACCGACTCGTTCTCGAAGGTCATGCCCGTCGAGCTGGGGAAGCTCGTTGCCAGGATCAATGCTGATGCGCGGGGGCG
CGGGAGGATCACCTGGTTGGTCGCCGACGTGAACATGGCGTGGGCCTTTCCCGTGGCGAAGAGGCTCGGCCTCCGGGCCG
CCGGGTTCTGCCCGTCGTCGGCGGCGATGTTCGCGACAAGGATCAGAATTCCGGAGATGATCAGCGATGGCATCCTTGAC
GACAGGGGCTGGCCGAGGCGGCGCGGCACGTTCCAGCTGGCTCCGGCGATGCCACCCATCGACACGTCGGAGTTCTCGTG
GAACCGCGCCGGCGACACCAGGGGCCAGCCGGTCATCTTCCAGTTGATCCTCCGGAACAACGCGGCCACGCACCTCGCCG
AGGCCATCGTGTGCAACACCATCCAGGAGCTGGAGCCCGGAGCCCTCGCGCTGTTCCCCAGCGTCCTTCCCGTGGGCCCG
CTCTCCTCCGACAAGCCGGTGGGAAGCTTCTGGACCGAGGACGCCTCCTGCGCGGCGTGGCTGGACGCGCAGCCGGCCAA
CTCCGTCGTGTACGTGGCGTTCGGCAGCTTCGCCGCCTACGACACCGCGCAGCTCGTGGAGCTGGCCGAAGGGCTCGCGC
TGACCTCCCGGCCTTTCCTGTGGGTGGTCAGGCCGGGGTCGGCGGGCGAGGAGCTCCTCGACCGGCTCCGCCGCCGCGCC
GCGCCGCGCGGGCGCGTGGTGAGCTGGTGCCCGCAGCGGCGCGTGCTGGCGCACCCCGCGGTCGCCTGCTTCCTGACGCA
CTGCGGCTGGAACTCGACGATGGAGGCCGTGGCCAACGGCGTGCCGCTCCTGTGCTGGCCATACTTCACCGACCAGTTCC
TGAACCAGAGCTACATCTGCGACGTGTGGAGGACGGGGATCAAGGTGCCGCGGCCGGCCGGCGGCGGGACGACGACGGGG
CTCGTGGGAAGGGACGTGGTGCGGGGGAAGGTGGAGGAGCTGCTCGGCGACGCGGGGACGAAGGCGAGGGCGCTCGCGCT
ACGGGACCTCGCCCGGCGGGCCGTCGGCGAGGACGGGTCGTCGCGCCGGAATCTCGAACGATTCGTGGACCTCGTGAAAG
GATCTGCGACCTGA

Alignment

ORF - retro_sita_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 95.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPHVLALPFPAQGHIIPLMQLSHRLVEHGIEVTFVNTEANHTLVLDAMAANGAGCPSLDGIRLVGVPD
          MAA..VL.LP.PAQGH.IP.M.LSH.LVEHG...TFVNTE.NH.L.L.A.A........L.G...V.VPD
Retrocopy MAATRVLVLPYPAQGHVIPMMELSHSLVEHGVKGTFVNTELNHGLILGALASRDS---VLGGVDMVSVPD

Parental  GLADGDDRKDLGKLVDALSQHMPCYLEELVGRI--EASGGTKISWLVADEGMGWAFEVAKKLGIRAACFW
          GL..G.DRKDL..L.D..S..MP..L..LV.RI...A.G...I.WLVAD..M.WAF.VAK.LG.RAA.F.
Retrocopy GLGCGEDRKDLARLTDSFSKVMPVELGKLVARINADARGRGRITWLVADVNMAWAFPVAKRLGLRAAGFC

Parental  TGSAAFLASMLRIPQLIQDGVIDEKGWPKRQETFQFAPGMPPLHTSHLSWNNAGAPKDQPAIFQLVVRNN
          ..SAA..A...RIP..I.DG..D..GWP.R..TFQ.AP.MPP..TS..SWN.AG....QP.IFQL..RNN
Retrocopy PSSAAMFATRIRIPEMISDGILDDRGWPRRRGTFQLAPAMPPIDTSEFSWNRAGDTRGQPVIFQLILRNN

Parental  EAKDLAEVTVCNSFGDAEPAAFKLYPDILPVGPLFADVQFKKPVGQFLPEDARCLEWLDAWPDRSVVYVA
          .A..LAE..VCN.....EP.A..L.P..LPVGPL..D....KPVG.F..EDA.C..WLDA.P..SVVYVA
Retrocopy AATHLAEAIVCNTIQELEPGALALFPSVLPVGPLSSD----KPVGSFWTEDASCAAWLDAQPANSVVYVA

Parental  FGSFTVFNPHQFEELALGLELTGRPFLWVVRPDFVAGLSKPWLDEFQRRVGDSGLIVSWCPQQQVLAHRA
          FGSF......Q..ELA.GL.LT.RPFLWVVRP..........LD...RR....G..VSWCPQ..VLAH.A
Retrocopy FGSFAAYDTAQLVELAEGLALTSRPFLWVVRP---GSAGEELLDRLRRRAAPRGRVVSWCPQRRVLAHPA

Parental  VACFVSHCGWNSTMEGVRNGVPFLCWPYFTDQFQNESYICNVWRTGLAVVRGADGVVTKEELSGKVERVI
          VACF..HCGWNSTME.V.NGVP.LCWPYFTDQF.N.SYIC.VWRTG..V.R.A.G..T.......V.R..
Retrocopy VACFLTHCGWNSTMEAVANGVPLLCWPYFTDQFLNQSYICDVWRTGIKVPRPAGGGTTTGLVGRDVVRGK

Parental  GDEGIRERVGALRDAARRSIA
          ..E.........R..A.R..A
Retrocopy VEELLGDAGTKARALALRDLA

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_3 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	Si035607m.g	1 retrocopy	retro_sita_3 ,