RetrogeneDB ID: retro_sita_6

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 1:3738357..3739680(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si017224m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si006418m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_6
ATGGAGAGGCTCCGGTGGAGCCGCCCCGGCTCCCTCCTCGTCCTCGCGGCGGCGTTCCTGGCGTCCGCCGCGGCGTCGAG
CGCCACCAGCATCGCCGACTGGGACGAGCACTGGCAGAAGCGCCGGGAGCTGGCCGAGGCGTCGGCCCGGGAGGCGTACA
AGCCCGACCCCTTCAACGTCACCAACAGCTTCAACGCCGCCGTGCACAGGTCCACCAGCCCGCGGCGCGAGATGCGGGAG
AAGAAGAAGAAGTCCAACGGCCCGTGCCGCGCCACCAACCCCATCGACAAGTGCTGGCGCTGCCGCAAGAACTGGGCCAC
GGACCGGCAGCGCCTGGCCCGCTGCGCCAGGGGCTTCGGCCGCGCCGCTACCGGCGGGCTCGGCGGCAAGATCTACGTCG
TCACCGACCCGACCGACGCCGACGTGGTGAACCCCCGCCCGGGGACGCTCCGGTGGGGCGCCATCCAGCCCGGCCCGCTC
TGGATCATCTTCGCCAGGTCCATGATCATCCAGCTCTCGCAGGAGCTCCTCGTCAGCAGCGACAAGACCATCGACGGCCG
CGGCGCGCAGGTCCACATCGCCAACGGCGGCGGCATCACCGTGCAGTTCGCGCGGAACGTCATCATCCACGGCCTCCACG
TGCACGACGTGAAGCACACCGACGGCGGGCTGATGCGGGACTCGCCGACGCACATGGGGCCCCGGACCAAGGCCGACGGC
GACGGCATCTCGCTGTTCGGCGCCACCGACGTGTGGATCGACCACATCTCCATGTCCAACTGCGAGGACGGGCTCATCGA
CGTCGTGCAGAGCTCCACGGGGGTCACCATCTCCAACTGCCACTTCACCAACCACAACGACGTGATGCTCTTCGGCGCCA
GCGACTCGTACCCGCAGGACCAGGTGATGCAGATCACCGTCGCCTTCAACCACTTCGGCAGGGGGCTCGTGCAGCGGATG
CCGCGCTGCCGGTGGGGCTTCTTCCACGTCGTCAACAACGACTACACGCACTGGCTCATGTACGCCATTGGAGGGAGCAA
CGCGCCTACCATCATCAGCCAGGGGAACAGGTACATCGCGCCGCCCAACATCGCCGCCAAGTTGATCACCAAGCACTACG
CCGACGAGGGGGTGTGGAAGAACTGGGTGTGGCACACGGAGGACGACCTCTTCATGAACGGCGCCGTCTTCCAGCCCTCC
GGCGGGGCGGTCCCCAGGAAGATCAACAAGAAGGAGTGGGTCAAGCCCAAGCCGGGATCCTACGTCACCAGGCTCACACG
CTTCTCCGGCACCTTGTCCTGCATCCCCGGCAGAAAGTGCTGA

Alignment

ORF - retro_sita_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.21 %
• Parental protein coverage: 99.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGFRWSRPGSFVLYAVVLLLSAAVSEANIGEFDDYWRQRKLMADAAAEATYQHDPIEVPNQLNRAVHRSI
          E..RWSRPGS..L......L..A.........D..W..........AEA.........P...........
Retrocopy ERLRWSRPGS-LLVLAAAFLASAAASSATSIAD--WDEHWQKRRELAEASAREAYKPDPFNVTNSFNAAV

Parental  KKEDISTRREMLGQKKGKMNGPCKATNPIDRCWRCRKDWATDRKRLARCAQGFGRNTTGGLAGKFYVVTD
          .....S.RREM...KK.K.NGPC.ATNPID.CWRCRK.WATDR.RLARCA.GFGR..TGGL.GK.YVVTD
Retrocopy HRST-SPRREMR-EKKKKSNGPCRATNPIDKCWRCRKNWATDRQRLARCARGFGRAATGGLGGKIYVVTD

Parental  GTDDDVVNPRPGTLRWAVIQIEPLWITFAKTMIITLKEELIIRGDKTIDGRGVQVRIANGAQLTVQFANN
          .TD.DVVNPRPGTLRW..IQ..PLWI.FA..MII.L..EL....DKTIDGRG.QV.IANG...TVQFA.N
Retrocopy PTDADVVNPRPGTLRWGAIQPGPLWIIFARSMIIQLSQELLVSSDKTIDGRGAQVHIANGGGITVQFARN

Parental  VIIHNIHINDIISSNKNGGNIRDSPDHFGWRTVSDGDGITVFGSTNVWLDHLSLSNCQDGLIDVIAKSTG
          VIIH..H..D.......GG..RDSP.H.G.RT..DGDGI..FG.T.VW.DH.S.SNC.DGLIDV...STG
Retrocopy VIIHGLHVHDV--KHTDGGLMRDSPTHMGPRTKADGDGISLFGATDVWIDHISMSNCEDGLIDVVQSSTG

Parental  VTISNCHMTNHNDVMLFSSSDKHPEDQIMQITVAFNHFGRGLVQRMPRCRWGFFHVVNNDYTHWLMYAIG
          VTISNCH.TNHNDVMLF..SD..P.DQ.MQITVAFNHFGRGLVQRMPRCRWGFFHVVNNDYTHWLMYAIG
Retrocopy VTISNCHFTNHNDVMLFGASDSYPQDQVMQITVAFNHFGRGLVQRMPRCRWGFFHVVNNDYTHWLMYAIG

Parental  GSKAPTIISQGNRYIAPPNLAAKQVTKQHDAPESEWKNWVWHSEDDLFMEGAYFTVTGGQINRQFNKKDL
          GS.APTIISQGNRYIAPPN.AAK..TK.H.A.E..WKNWVWH.EDDLFM.GA.F...GG...R..NKK..
Retrocopy GSNAPTIISQGNRYIAPPNIAAKLITK-HYADEGVWKNWVWHTEDDLFMNGAVFQPSGGAVPRKINKKEW

Parental  IKPKPGSYVTRLTRFAGSLDCKPGKPC
          .KPKPGSYVTRLTRF.G.L.C.PG..C
Retrocopy VKPKPGSYVTRLTRFSGTLSCIPGRKC

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_6 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC06G17690	1 retrocopy	retro_opun_11,
Setaria italica	Si006418m.g	1 retrocopy	retro_sita_6 ,