RetrogeneDB ID: retro_sita_41

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 3:22276593..22279827(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si024749m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si021302m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_41
ATGGCCACGGCCTCGGAGGGCGGCGAGGGGCAGCTCAAGACGTGGGTCTCGGACCGGCTTATGGCGCTGCTCGGGTACTC
CCAGGGCATCGTGCTCCGGCTCGTGCTCCGGCTCGCGCGGGAGTGCGCCTCCGCGGGGGACCTCGCGGCGCGGCTGGTCG
ACCTCGGCGGGTTCCCCTCCTCCCCCGACACAGCCGCCTTCGCCGCGGACGTCTACGGAAGGCTGCCGCGCCCCAGCAAG
CAGGGCGCGGCGGGGGTCGGCGAGTACCAGAGGCAGGTGCAGGACGCGGCGGCGCTGGCGAGGAAGCAGAGCGAGTTCAA
GCTGCTCAACGATGACGTCGACGACGAGGATGCTGGCGTCGCCGCGGCGTCCTGTAACAGCAGCAGCGGGAAGCGTTTCA
GGAAGAAGGGCGTGACCCATGACCATGAGGACGAAGAGGAGGGGGCCGCATTGTCCGATTCTGATCGGAAGGTGCGCCGG
CGGCGGTGCCCGGAGTCGGACGAGGACGCCGGCGATACTGACGAGGAGGAAGAGATGAGGCGTGATCAGGCTGACAGGGC
CCAGCTCGAACGGAACATCCGGGCGCGCGATGAGGCGAGCACGAGGAAACTGATGGACCGGAAGCCGTCCAAGCGCGAGC
AGGACGAGAGAGCTCGCCGGTCCGAGGCGATGGACAGGGGCGACACCTCGGAGCTCAGGCGGTCCTCCCGTCGCGCGTAC
CTGGAGATGCGTAAGAAGAAGAAGGTGGAGGAGTTGCGGGACGAGATCGTCGACGACGAGCTCTTGTTCGGCGGCGTCAG
ACAGACGGACGCCGAGGAGAGGGAGTTGAAGCGCAAGAAGGAAATCTACGGCCTTGTCCACGGCCGAGCCAGTCAAGAAG
AGGAAGGCGCCGGCGACTACTACAGGATGCCTGACGCCTACGACGACGCCGCGAACGTGGACCAGGGGAGGAGGTTCTCG
GTGGCGAGACGGCGGCACGACGACGACGCTGATGCGGGAGGCGGCAAGGGGAGGGCTTTCTCGGAGGAGTCCTGGGAAGA
GCAGCAGATCAGGAAGTCCCATCTGCAGTTTGGAGCGAAGGATCGCGGCCACGCCAGTGATGAATACGAGCTCGTGTTCG
ATGACGCCATCGAGTTCGTCAAGTCCTTGGCGATGGCTGGAACCGAGCCGGAGGATGACACGGACGAACTGGCGGAGGAA
ATTGATGCCAAGGTCATGTTGCAGATGGAGCTCCAAGACCAGAGGAAGACTCTCCCTGTGTACAAGTTCAAGGACGAGCT
CCTCAAGGCCATTGCCGACCATCAGATTATCATTGTCGTCGGAGAGACCGGCTCCGGTAAGACGACGCAGATACCACAGT
ATCTTCACGAGGCCGGGTACACCGCCAATGGGCGGAAGATCGCGTGCACTCAGCCACGCCGCGTGGCCGCGATGAGCGTG
GCGGCGAGGGTCGCGCAGGAGATGGGCGTCAAACTCGGCCACGAGGTCGGGTACTCTATCCGCTTCGAGGACTGCACGTC
GGAGAAGACGGTGGTCAAGTACATGACCGACGGGATGCTGCTACGCGAGTTCCTTGGCGAGCCTGACCTGGGCAGCTACG
GCGTCGTGATCGTGGACGAGGCGCACGAGCGCTCCATCTCCACGGACATCCTCCTCGGCCTCGTCAAGGACGTCGCCCGC
TTCCGGCCGGACCTGAAGCTGCTCATCTCCAGCGCTACGCTCAACGCGGACAAGTTCAGCGACTTCTTCGACATGGCGCC
GGTGTTCAAGATCCCCGGGAGGCGGTACAAGGTGGACATCCACTACACGGTGGCGCCGGAGGCCGACTACGTGGACGCGG
CCGTGGCCACGGTGCTGCAGCTGCACGTCACGCAGCCCTCCGGAGACATCCTGCTGTTCCTCACGGGGCAGGAAGAGATC
GAGACGGTGGAGGAGATCCTCCGGCGCCGGACAAGGGGGCTGGGCACCAAGATCGCGGAGCTGGTGATCTGCCCCATCTA
CGCGAACCTGCCGACGGAGCTCCAGGCCAAGATCTTCGAGCCGGCGCCGCCGGGCGCGCGGAAGGTGGTGCTCGCCACCA
ACATCGCCGAGACGTCGCTGACCATCGACGGGATCAGCTACGTGGTCGACCCGGGGTTCTGCAAGGTGAAGTCGTACAGC
CCGCGCACGGGTACCGAATCGCTGCTCGTCCAGCCTATCTCCAAGGCGTCGGCCGACCAGCGCGCCGGCCGGTCGGGGCG
CACCGGCCCCGGCAAGTGTTTCCGCCTATTCACGGAGCACAGCTACAACAAGGACATGGAGGACGAGACGGTCCCCGAGA
TCCAGCGGAGCAACCTGGCCAGCGTGGTGCTCTCGCTCAAGGCGCTGGGGATCAACGACTTGGTGAGCTTCGACTTCATG
GACCCGCCGGCGTCGGAGGGTCTCCTCAGGGCGCTGGAGGACCTCTTCGCCCTCGGCGCGCTCAACAGCCGCGGCGAACT
GACCAAGACTGGGCGGCGGATGGCGGAGCTCCCGCTCGACCCCATGCTGGCCAAGGCGATCGTGGCGTCGGAGCGGTACG
GGTGCTCTGAGGAGTTGCTCACCGTCGCGTCCATGCTGTCGGCCGGGAACGCCGTCTTCTACCGGCCCAAGGACAGGGCG
CTGGTCGCCGACGCCGCACGGCAGCGCTTCAACGCGGGAGGCAACGCCGGGGACCACGTCGCGCTGCTCAACGTGTACAC
CGAGTGGGAGCAGTCCGGGCACTCGGCGCAGTGGTGCCTCGACCACTTCGTGCAGTCGCGCACCATGCGGCGCGCGCGGG
ACGTGCGGGAGCAGCTGGAGGCGCTGATGGAGAGGGTGGAGATCGAGCGCCGGTCCTGCGCCGGCGACCTCGACACGGTC
AGGAAGGCCATCACGGCGGGGTTCTTCCGCAACACCGCGCAGCGGCGGAGGGACGGGTTCTACCGGACCCTCAAGAGCTG
GCGGACGGTGTTCGTGCACCCGAGCTCCGGGATGGCGCGGGTGGTCCCGCCGCCGCGTTGGGTGGTGTACCACGAGCTGG
TGGAGACGACCAAGGAGTACATGAGGCAGGTGACGGAGCTCAAGCCGGAGTGGCTGCTGGAGATCGCGCCGCACTACTAC
CAGGAAAGCAACCTCAACAAGCCGGAGCCGAAGAAGGCCAAAGCGCATGTGCAGGGTGCCGCAGTAGCCGCGGAGAAGCC
GAGTCTGAGTCTTAAGGACTTTTTCAATGTGTAG

Alignment

ORF - retro_sita_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.87 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPEAYDMGENVNQEKRFSVAIQRYKDP-EAKDKMNPFAEQEAWEEHQIGKSKLQFGSKDRKRSSDDYQYV
          MP.AYD...NV.Q..RFSVA..R..D...A..........E.WEE.QI.KS.LQFG.KDR...SD.Y..V
Retrocopy MPDAYDDAANVDQGRRFSVARRRHDDDADAGGGKGRAFSEESWEEQQIRKSHLQFGAKDRGHASDEYELV

Parental  FEDSIDFVKSSVIEGTQPEYNSDQ--EDIDAKDILKRELQDERKTLPIYKFRDELLKAVEEYQVIVIVGE
          F.D.I.FVKS....GT.PE...D...E.IDAK..L..ELQD.RKTLP.YKF.DELLKA....Q.I..VGE
Retrocopy FDDAIEFVKSLAMAGTEPEDDTDELAEEIDAKVMLQMELQDQRKTLPVYKFKDELLKAIADHQIIIVVGE

Parental  TGSGKTTQIPQYLHEAGYTAKG-KVACTQPRRVAAMSVSARVSQEMGVKLGHEVGYSIRFEDCTSEKTII
          TGSGKTTQIPQYLHEAGYTA.G.K.ACTQPRRVAAMSV.ARV.QEMGVKLGHEVGYSIRFEDCTSEKT..
Retrocopy TGSGKTTQIPQYLHEAGYTANGRKIACTQPRRVAAMSVAARVAQEMGVKLGHEVGYSIRFEDCTSEKTVV

Parental  KYMTDGMLLREFLGEPDLASYSVVMVDEAHERTLSTDILFGLVKDISRFRPDLKLLISSATLDAEKFSDY
          KYMTDGMLLREFLGEPDL.SY.VV.VDEAHER..STDIL.GLVKD..RFRPDLKLLISSATL.A.KFSD.
Retrocopy KYMTDGMLLREFLGEPDLGSYGVVIVDEAHERSISTDILLGLVKDVARFRPDLKLLISSATLNADKFSDF

Parental  FDSAPIFKIPGRRYPVEIHYTKAPEADYIDAAIVTVLQIHVTQPPGDILVFLTGQEEIETVDEILKHRTR
          FD.AP.FKIPGRRY.V.IHYT.APEADY.DAA..TVLQ.HVTQP.GDIL.FLTGQEEIETV.EIL..RTR
Retrocopy FDMAPVFKIPGRRYKVDIHYTVAPEADYVDAAVATVLQLHVTQPSGDILLFLTGQEEIETVEEILRRRTR

Parental  GLGTKISELIICPIYANLPTELQAKIFEPTPEGARKVVLATNIAETSLTIDGIKYVIDPGFCKIKSYNPR
          GLGTKI.EL.ICPIYANLPTELQAKIFEP.P.GARKVVLATNIAETSLTIDGI.YV.DPGFCK.KSY.PR
Retrocopy GLGTKIAELVICPIYANLPTELQAKIFEPAPPGARKVVLATNIAETSLTIDGISYVVDPGFCKVKSYSPR

Parental  TGMESLLINPISKASANQRAGRSGRTGPGKCFRLYTSYNYMHDLEDNTVPEIQRTNLANVVLTLKSLGIH
          TG.ESLL..PISKASA.QRAGRSGRTGPGKCFRL.T...Y..D.ED.TVPEIQR.NLA.VVL.LK.LGI.
Retrocopy TGTESLLVQPISKASADQRAGRSGRTGPGKCFRLFTEHSYNKDMEDETVPEIQRSNLASVVLSLKALGIN

Parental  DLVNFDFMDPPPSEALLKALEQLFALSALNSRGELTKTGRRMAEFPLDPMLSKMIVASEKYKCSDEVISI
          DLV.FDFMDPP.SE.LL.ALE.LFAL.ALNSRGELTKTGRRMAE.PLDPML.K.IVASE.Y.CS.E....
Retrocopy DLVSFDFMDPPASEGLLRALEDLFALGALNSRGELTKTGRRMAELPLDPMLAKAIVASERYGCSEELLTV

Parental  ASMLSIGNSIFYRPKDKQVHADNARLNFHT-GNVGDHIALLNVYSSWKETDYSTQWCYENYIQVRSMKRA
          ASMLS.GN..FYRPKD....AD.AR..F...GN.GDH.ALLNVY..W.....S.QWC.....Q.R.M.RA
Retrocopy ASMLSAGNAVFYRPKDRALVADAARQRFNAGGNAGDHVALLNVYTEWEQSGHSAQWCLDHFVQSRTMRRA

Parental  RDIRDQLEGLMERVEIEICSNASDLDAIKKAITSGFFHHSARLQRDGTYKTVKNPQTVHIHPSSGLAEI-
          RD.R.QLE.LMERVEIE..S.A.DLD...KAIT.GFF...A...RDG.Y.T.K...TV..HPSSG.A...
Retrocopy RDVREQLEALMERVEIERRSCAGDLDTVRKAITAGFFRNTAQRRRDGFYRTLKSWRTVFVHPSSGMARVV

Parental  -RPRWVVYHELVLTTKEFMRQVTELKPEWLVEIAPHYYQLKDVDDSGTKK
          ..PRWVVYHELV.TTKE.MRQVTELKPEWL.EIAPHYYQ.........KK
Retrocopy PPPRWVVYHELVETTKEYMRQVTELKPEWLLEIAPHYYQESNLNKPEPKK

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_41 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 16 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65,
Brassica oleracea	Bo5g087070	1 retrocopy	retro_bole_7,
Brassica rapa	Bra010168	1 retrocopy	retro_brap_26,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4,
Glycine max	GLYMA06G21821	1 retrocopy	retro_gmax_7,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Solanum tuberosum	PGSC0003DMG402024649	1 retrocopy	retro_stub_33,
Prunus persica	PRUPE_ppa000714mg	1 retrocopy	retro_pper_32,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41 ,