RetrogeneDB ID: retro_sita_36

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 3:10822765..10824634(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si024932m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si004698m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_36
ATGGGGTACTCCCTGCCCCGCGCCGCGGCCTTCGCCGTGGCCCTCCTCCTCCTGGCCTCCTCCGGCGAGGCGTTCTTCGA
CATCTTCAACATCTTCCGCCCGCGCTCCGAGAGCGACGACTTCTTCCAGAACGCCTTCGATGGCTCGCAGGAGCAGGCGG
TGCCGACGCAGACAGAGCACGAAGAGCAGGGCGCCGCGCCGGCCACCGCCACGGGCCTCACCAGGGTGCCGCCCTCGGGC
CCGCCCAGCAAGGCCGCGCAGGACACGGTCGAGCTCGCCGCCGACACCGGCGGCGGGCCGGTCGGCGAGTGGACCATCGT
CAGCGAGAACTCCGGCGTGTCGGCCATGCACATGGTCCTCATGCGCCACGGCAGGGCCGTCATGTTCGACACCAGCACCA
CTGGCCGGTCGCTCATGCGGCTGCCCCAGGACAACTGCCGCATCGACCCGCGCGCCAAGGAGGAGGGCACCATGGATTGC
TGGGCGCACGCCGTCGAGTTCGACTACCACACCGGCGGCCTCCGCCCTCTCAAGATCCTGACGGACACCTGGTGCTCGTC
GGGCGCGTTCGACGCGGACGGCAACCTTGTGCAGACCGGCGGCTACTTCGAGGGCGAGAAGGTCGTGAGGGTGCTGAGCC
CGTGCGACACCTGCGACTGGCTGGAGCACCCCAACAGCTTCGCGGAGGGGAGGTGGTACGCGACGACGCTGGTGCTCCCG
GACGGCCGGTTCATCGTGTTCGGCGGCCGCCGCGCCTTCAGCTCCGAGCTCGTCCCGATGCCGGGGAGGACCAACGACAG
GGCCACCTACATGCCGTTCCTCCGCGAGACCACCGACGACGTCGAGAACAACCTGTACCCGTTCGCGAACCTCCTCCCCA
GCGGCGAGCTCTTCCTCTTCGCCAACAACCGCTCCGTCATCTTCGACCACAGGGCCGGCAGGATCGTGCGCGAGCTCCCG
CAGCTGGGCGGTGGGAGCCGCAACTACCCGGCGTCCGCCATGTCTGCGCTCCTCCCGCTCGACCTCCGCAACGCCACCGG
CGGCGCCGACCCCGAGCCGGTGGTCATCATCTGCGGCGGGACGTTCAAGAAGGCCTTCAGGTTCGGCGAGAACAACACGT
TCCTGCCCGCGCTCCGCGACTGCGCCCGCATCAACCTGGCCGCGCTCGACGCGCAGTGGGAGACCGAGGACATGCCCGTC
GGCCGCGTCATGGGCGACATGCTCATCCTCCCCACCGGCGACCTGCTGCTCCTCAACGGCGCCGCCAAGGGCTGCGCCGG
CTGGGGCTTCGGCCGGCAGCCGGTCCTCACCCCGGTCCTGTACTCGCCGCGGAAGGAGAAGGGGTCGCGGTTCCGGGCGC
TGGCGTCGTCGACCATCGCGCGCATGTACCACTCCACCAGCGCCGTGCTGCCCGACGCCACCGTGCTCGTCGCCGGCGGC
AACACCAACACCGCCTACAACTTCAGCGACGTGGACTTCCCCACCGAGGTGCGCGTGGAGCGGTTCTGCCCGCCGTACCT
GAGCAAGGATCACGCCGCAACCCGGCCGGTGATCGACGCAGCGTCGGTGCCCGCGGGAGGGATGCGGTACGGGTCCCCGT
TCACGTTCCGATTCTCCATGCCCTCCGAGCCCGTGGGGGAGGCGGACGTGAAGGTCACCATGTACGCGCCGCCCTTCACC
ACGCACGGCTACTCCATGAACCAGCGGCTGCTGATCCTGTCCGTGACCGCGTTCAGGGAGGAGGGGCGGAGCTACACGGT
GACCGTGGACGCGCCCGGGAAGCCGGAGCTCGCGCCGCGGGGGTACTACCTGGTGTTCGTGGTGGCCAAGGGCGTGCCGA
GCGTGGCTGCGTGGGTGAAGATTCTGTGA

Alignment

ORF - retro_sita_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.17 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLRAAVLSAALLALAAAGAEAHSVSEFLNIFRPRNEHD-YFHNANQGQQEENVVPRASDQQSLIAAPVSQ
          L.RAA....ALL.LA..G..........NIFRPR.E.D..F.NA..G.QE...VP.........AAP...
Retrocopy LPRAAAFAVALLLLASSG---EAFFDIFNIFRPRSESDDFFQNAFDGSQEQ-AVPTQTEHEEQGAAPATA

Parental  SGLMKVPARSAPTAAGQDTITIPVDDHTAGNAGAWSTITENAGVSAMHMVIMRNDRAIMFDTVTTGPSLL
          .GL..VP....P..A.QDT.....D....G..G.W....EN.GVSAMHMV.MR..RA.MFDT.TTG.SL.
Retrocopy TGLTRVPPSGPPSKAAQDTVELAADTG-GGPVGEWTIVSENSGVSAMHMVLMRHGRAVMFDTSTTGRSLM

Parental  RLPKGNCRLDLRSKQQGAQDCAAHAVEFDYATGGVRALKILTDVWCSSGALDAEGNLVQTGGYFEGEKVV
          RLP..NCR.D.R.K..G..DC.AHAVEFDY.TGG.R.LKILTD.WCSSGA.DA.GNLVQTGGYFEGEKVV
Retrocopy RLPQDNCRIDPRAKEEGTMDCWAHAVEFDYHTGGLRPLKILTDTWCSSGAFDADGNLVQTGGYFEGEKVV

Parental  RYLSPCGNCDWREFPASLAEGRWYGTQQILPDGRSIVLGGRRAFSYEFVPAEGQANTQANPLQILRDTTD
          R.LSPC..CDW.E.P.S.AEGRWY.T...LPDGR.IV.GGRRAFS.E.VP..G..N..A.....LR.TTD
Retrocopy RVLSPCDTCDWLEHPNSFAEGRWYATTLVLPDGRFIVFGGRRAFSSELVPMPGRTNDRATYMPFLRETTD

Parental  DVENNLYPFVHLLTDGTLFIFANDRSVVFDYRNGQVVRELPVLPGGGRNYPASGMSALLPLDLRR---GD
          DVENNLYPF..LL..G.LF.FAN.RSV.FD.R.G..VRELP.L.GG.RNYPAS.MSALLPLDLR....G.
Retrocopy DVENNLYPFANLLPSGELFLFANNRSVIFDHRAGRIVRELPQLGGGSRNYPASAMSALLPLDLRNATGGA

Parental  VLSPEVIVCGGTPKNAFKLGETNTFNPALKDCARINPLKPDARWAIDQMPVARTMGDLLILPTGDLLMLN
          ...P.VI.CGGT.K.AF..GE.NTF.PAL.DCARIN....DA.W....MPV.R.MGD.LILPTGDLL.LN
Retrocopy DPEPVVIICGGTFKKAFRFGENNTFLPALRDCARINLAALDAQWETEDMPVGRVMGDMLILPTGDLLLLN

Parental  GAARGCSGWGFARQPVLTPLLYSPRQPRGKRFRALAATAIARMYHATSAVLPDATVLVAGSNTNSAYNFS
          GAA.GC.GWGF.RQPVLTP.LYSPR...G.RFRALA...IARMYH.TSAVLPDATVLVAG.NTN.AYNFS
Retrocopy GAAKGCAGWGFGRQPVLTPVLYSPRKEKGSRFRALASSTIARMYHSTSAVLPDATVLVAGGNTNTAYNFS

Parental  GVDFPTEVRVERFTPPYLAAGRAHNRPVIDAATVPGGGMAYGSQFTLQFTTPALPVAETDMKVTMYAPPF
          .VDFPTEVRVERF.PPYL....A..RPVIDAA.VP.GGM.YGS.FT..F..P..PV.E.D.KVTMYAPPF
Retrocopy DVDFPTEVRVERFCPPYLSKDHAATRPVIDAASVPAGGMRYGSPFTFRFSMPSEPVGEADVKVTMYAPPF

Parental  TTHGFSMNQRLLVLSVTAFVPKGPNRYTITVGAPGKPELAPPGYYLLYVMAQGVPSKAVWVKV
          TTHG.SMNQRLL.LSVTAF...G...YT.TV.APGKPELAP.GYYL..V.A.GVPS.A.WVK.
Retrocopy TTHGYSMNQRLLILSVTAFREEG-RSYTVTVDAPGKPELAPRGYYLVFVVAKGVPSVAAWVKI

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_36 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004194	1 retrocopy	retro_oind_16,
Brachypodium distachyon	BRADI2G46477	1 retrocopy	retro_bdis_13,
Oryza glumaepatula	OGLUM01G30230	1 retrocopy	retro_oglu_1,
Oryza meridionalis	OMERI01G24080	1 retrocopy	retro_omer_13,
Oryza glaberrima	ORGLA01G0215900	1 retrocopy	retro_ogla_7,
Oryza sativa japonica	OS01G0677000	1 retrocopy	retro_osat_22,
Setaria italica	Si004698m.g	1 retrocopy	retro_sita_36 ,