RetrogeneDB ID: retro_sita_17

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 4:35880797..35882423(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si007876m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si007904m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_17
ATGGAGCTGGCGGCAGCGGCCTCGCCGGCGCTTGAAGCTCCCTTGCCCTCCTCCTCGACTGTCCTCCAAGTGTTACTGCT
CATGGTGATGCTCGTGTACCTCGTCCAAACCCTCATGGCGCGGCGGAAGAGCACGTGCACCGCGCCGCTCCCGCCAGGGC
CGACGCCATGGCCCGTTGTCGGCAACCTGCCGGAGATGCTGCTCAGCGACAAACCGGCGTTCAGGTGGATCCACCTCATT
ATGATCAAAATGGGCACCGACATCGCCTGCGTCAAGCTAGGCGGCGTCCACGTGATCCCGATCACCTGCCCCATGATCGC
ACGCGAGGTGCTCAAGAAGCAGGACGCCAACTTCGCCTGCCGGCCGCTGAGCTTGGCCTCCAAGACATTCAGCAGAGGCT
ACATGGACGCCGTGATGTCCCCCTACGGCGACCAGTGGAGGAAGATGCGCCGCGTGCTAGCCTCCGAGGTCGTTTGTCCT
TCCCGCCACAGGTGGCTCCACGACAAGCGCGCCGCCGAGGCCGATAACCTCACCCGCTTCGTCTACAACCTCGCCGGCGG
AGCGGGGTCCGGCGGCGCCGCCGTCGACGTCAGGCACGTCGCGCGCCACTATTGTGGGAACGTCGTCCGCCGCCTCGTCT
TCAATAGGCGCTACTTCGGCGAGCCGCGGCCCGACGGCGGCCAAGGCCCGCTGGAGGTGCAGCACGTGGATGCGGTGTTC
ACCTCCCTGGGGCTCCTCTACTCCTTCTCCGTCTCCGACTACCTCCCCTGGCTGCTGGGCCTCGACCTCGACGGCCACGA
GAAGATGGTCAGGGAGGCCCAGGAGACGGTGAGCAGGCTGCACGACACGTTCATCAACGAGCGGTGGCGGCAGTGGAAGA
GCGGCGAGAGGCAGGAGCTCGAGGACCTCCTCGACGTGCTCATCACGCTCAAGGATGCCGAGGGCAAACGATCCGTGCTC
ACCGTCGATGAGGTCAGAGCTCAGTTGCAGGACATCACGTTCGCGGCCATGGACAACCCATCGAACGCGGTGGAGTGGGC
GATGGCCGAGATGGTGAACGCTCCGGAGACGATGAGGAAGGCGGTGGCGGAGCTCGATGCCGTCGTCGGCCGGGACCGAC
TGGTGCAGGAGTCCGACATACCGCGGCTCAACTACCTCAAGGCCTGCATCCGCGAAGCGTTCCGCCTGCACCCCGTGGCG
CCGTTCAACGTCCCCCATGTCGCGCTCGCCGACGCCACCGTCGCCGGCTACCACGTCCCCAAGGGCAGCCACGTCATCCT
CAGTCGAATCGGCCTCGGCCGCAATCCTGCCGTCTGGGACGATCCGCTCCGGTTCGACCCTGACCGACACCTCGACGCCA
ATCCCGAGGCGGATGTCACGCTCGCCGAGAACGACCTGCGGTTCATCTCTTTCAGCACCGGTCGCCGCGGCTGCATTGCC
GCTTCACTCGGCACCGCCATGAGTGTCATGCTCTTTGGCAGGCTCTTGCAGGGGTTCGCCTGGAGCAAGCCGGCCGGGAT
GGCGGCCATCGACCTCAGCGAGTCAAGGCACGACATGTTCATGGCCAAGCCGCTGGTGCTGAACGCCGAGCCACGGCTGC
CGGCGAACCTCTACTCGGCTATCTCT

Alignment

ORF - retro_sita_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.44 %
• Parental protein coverage: 98.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEATAAATSVLGAS-SLTSAILKALLLLVTMVCLVRTIRPQRKTKFTASLPPGPTPWPIVGNLPEMMLN-
          ME..AAA...L.A.....S..L..LLL.V..V.LV.T....RK...TA.LPPGPTPWP.VGNLPEM.L..
Retrocopy MELAAAASPALEAPLPSSSTVLQVLLLMVMLVYLVQTLMARRKSTCTAPLPPGPTPWPVVGNLPEMLLSD

Parental  KPAFRWIHHVMKDIGTDIACIKLGGVHVIPITCPAIAREVLRKQDTTFASRPLTFASETFSGGYRNAVLS
          KPAFRWIH..M...GTDIAC.KLGGVHVIPITCP.IAREVL.KQD..FA.RPL..AS.TFS.GY..AV.S
Retrocopy KPAFRWIHLIMIKMGTDIACVKLGGVHVIPITCPMIAREVLKKQDANFACRPLSLASKTFSRGYMDAVMS

Parental  PYGDQWRKMRRVLASEIVCPSRHKWLCSKRADEADNITRYVYSLV--KTKSGGAVDVRHVARHYCGNVIR
          PYGDQWRKMRRVLASE.VCPSRH.WL..KRA.EADN.TR.VY.L.......G.AVDVRHVARHYCGNV.R
Retrocopy PYGDQWRKMRRVLASEVVCPSRHRWLHDKRAAEADNLTRFVYNLAGGAGSGGAAVDVRHVARHYCGNVVR

Parental  RLVFNRRHFGEPQPDGGPGPLEVQHVDAVFRSLGLLYAFCVSDYLPWLLGLDLDGHEKMVKEANKIVNGL
          RLVFNRR.FGEP.PDGG.GPLEVQHVDAVF.SLGLLY.F.VSDYLPWLLGLDLDGHEKMV.EA...V..L
Retrocopy RLVFNRRYFGEPRPDGGQGPLEVQHVDAVFTSLGLLYSFSVSDYLPWLLGLDLDGHEKMVREAQETVSRL

Parental  HDKVIDERWRQWKSGERKEPEDFLDVLITLKAADGK-ALLTIEEVKAQSQDITFAAVDNPSNAVEWALAE
          HD..I.ERWRQWKSGER.E.ED.LDVLITLK.A.GK...LT..EV.AQ.QDITFAA.DNPSNAVEWA.AE
Retrocopy HDTFINERWRQWKSGERQELEDLLDVLITLKDAEGKRSVLTVDEVRAQLQDITFAAMDNPSNAVEWAMAE

Parental  TVNNPELLEKAAAELDGVVGRGRLVQESDIPWLCYLKACIREAFRLHPVAPFNVPHVALADATVAGYHVP
          .VN.PE...KA.AELD.VVGR.RLVQESDIP.L.YLKACIREAFRLHPVAPFNVPHVALADATVAGYHVP
Retrocopy MVNAPETMRKAVAELDAVVGRDRLVQESDIPRLNYLKACIREAFRLHPVAPFNVPHVALADATVAGYHVP

Parental  KGSHVILSRIGLGRNPAVWDDPLRFDPGRHIIPGDPTAEVTLCENELRFISFSTGRRGCIAASLGTAMSV
          KGSHVILSRIGLGRNPAVWDDPLRFDP.RH.....P.A.VTL.EN.LRFISFSTGRRGCIAASLGTAMSV
Retrocopy KGSHVILSRIGLGRNPAVWDDPLRFDPDRH-LDANPEADVTLAENDLRFISFSTGRRGCIAASLGTAMSV

Parental  MLFGRLLQCFTWSKQAAVTTIDLSESRNDTFMAKPLVLHAEPRLPAHLY
          MLFGRLLQ.F.WSK.A....IDLSESR.D.FMAKPLVL.AEPRLPA.LY
Retrocopy MLFGRLLQGFAWSKPAGMAAIDLSESRHDMFMAKPLVLNAEPRLPANLY

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_17 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	Si007904m.g	1 retrocopy	retro_sita_17 ,