RetrogeneDB ID: retro_sita_1

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 2:42753265..42754669(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si031920m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si032233m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_1
ATGGCTTCGCGCTCGCTCCTCGCCACGGTTTGCCTGCTGCTCCTAACGCTGCTTGGCGGCACCCTCGTCGAAGCACGTCC
AGCGCCACGGTCGCCGCACCGGAACGCACCAAGACGTCACCTCTGGACGACGGACGCGCCGGAGGGCAGTGCTGATGGCT
ACCCGAACACATGGTACGCGCACCGCAAACTCGGCGAGAAGAGCAAGCCCCCGAAGAACGCGACGACAAAGGGCGTCCAG
TTCGACGTCGGCAGCTTCGGAGCCACAGGCGACGGTCAGACCGACGACACCGGCGCGTTCCAGAATGCCTGGGCCCAGGC
CTGCTCCTCAGAACAACCCGCCGTCCTGCTCGTCCCCGCCGGAAAGAGCTACCTCGTCAAGGAGACCAGCCTGTCGGGGC
CGTGCAAGTCCAAGGTCACGTTCAAGCTCGAGGGAACCCTGGTGGCTCCGGAGGACAAGTCGGGCTGGAGCAAGCAAGGC
CACCCGCACTGGGTAAGCTTCAGCAACGTCGACAGCCTCACGGTGACCGGCAAGGGCGCCATGGACGGAAAGGGCAAGAC
GTCGTGGAAGAACTCGTGCCGCCGGAACCACAAGATGCCGTGCACCTTCGCGCCGGCGGCGCTCACCTTCTCGTCGTGCA
ACCACCTCAAGGTGGAAAACATAAAGCTGCTCAACGCCCCGCAGATCCACCTCTGGGTGGAGTTCTGCAGCGACGTGACG
CTGTCCCGCCTCACTATCGCGTCGCCCGGGGACAGTCCTGAGAACGATGGCATCCACGTGGCGCACAGCGACGGCGTCCG
CATCCTGGGCGCCAAGATCAAGGCCGGCGACGACTGCATCTCGATCGCCATGGGCACGACGAACCTGTACGCTACCAAGA
TCGAGTGCGGGCCGGGGCACGGGATCAGCGTCGGGAGCCTCGGGAAAGGGAGCACCAGGGCCGAGGTGTCCAACGTCACC
ATCGACGGCGCGCACGTGTCGGGCACGCTGTTCGGGGCCAGGATCAAGACGTGGCAGGGGGGCACGGGGTACGCCAGGGA
CATCAAGTTCCTCAACATGGTGATGGACAAGGTGAAGAACCCCATCGTCATCGACCAGAACTACTGCACGACGTCGGACC
CGTCCAAGCCAAAGGCGTGCAGCCAGAAGGAGTCCGCGGCGGTGGAGATCAGCAACGTGGAGTTCAGCAACATCAGGGGC
ACCAGCGTCAACAGGGATGCCATCAGGCTGCACTGCAGCGAGGCCTTCCCCTGCCGCGGCGTCGTGCTGCGGGACATCGA
ACTCAAGACGAGGGGAGGTGACGAGAAGAACGCCGCCACGAGCACCTGCGAGAACGCCGTGCTGGGCGAGACGAGCAACG
TTTCGCCGGCGCCGTGCTCGTCGGCGGCGACCAAAGAGGATTTG

Alignment

ORF - retro_sita_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.89 %
• Parental protein coverage: 89.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FNVRRYGAHGDGRHDDTRSIAKTWAAACSSSQSAVVLIPRGKRHLINHVTLSGPCKSSIMLMIEGTLMAP
          F.V...GA.GDG..DDT......WA.ACSS.Q.AV.L.P.GK..L.....LSGPCKS......EGTL.AP
Retrocopy FDVGSFGATGDGQTDDTGAFQNAWAQACSSEQPAVLLVPAGKSYLVKETSLSGPCKSKVTFKLEGTLVAP

Parental  PKGSHWSKKTNRHWIMFNDVDGLTIAGGGTIDGNGKIWWQNSCKTNSRPPCKQAPTALTFYSCKNLKLEN
          ...S.WSK....HW..F..VD.LT..G.G..DG.GK..W.NSC..N...PC..AP.ALTF.SC..LK.EN
Retrocopy EDKSGWSKQGHPHWVSFSNVDSLTVTGKGAMDGKGKTSWKNSCRRNHKMPCTFAPAALTFSSCNHLKVEN

Parental  LKLVNSQQIHMSVEDCSHVKIARLSITAPGTSPNTDGIHITRSKHVQVRDCTIKTGDDCMSIEDGTENLH
          .KL.N..QIH..VE.CS.V...RL.I..PG.SP..DGIH...S..V......IK.GDDC.SI..GT.NL.
Retrocopy IKLLNAPQIHLWVEFCSDVTLSRLTIASPGDSPENDGIHVAHSDGVRILGAKIKAGDDCISIAMGTTNLY

Parental  ASNIVCGPGHGISIGSLGDRGSRAHVVNVTVDTAWLYGTANGARIKTWQGGRGYAKNIVFENMVMGDVRN
          A..I.CGPGHGIS.GSLG....RA.V.NVT.D.A...GT..GARIKTWQGG.GYA..I.F.NMVM..V.N
Retrocopy ATKIECGPGHGISVGSLGKGSTRAEVSNVTIDGAHVSGTLFGARIKTWQGGTGYARDIKFLNMVMDKVKN

Parental  PIVIDQNYCDSATPCR----KQKSAVEV--SNVLFKNIRGTSASKEAIKLRCSTSVPCHGITLENVKLTL
          PIVIDQNYC....P.......QK....V..SNV.F.NIRGTS....AI.L.CS...PC.G..L....L..
Retrocopy PIVIDQNYCTTSDPSKPKACSQKESAAVEISNVEFSNIRGTSVNRDAIRLHCSEAFPCRGVVLRDIELKT

Parental  KGGD--GVAKSTCENAKWRKSGTVTPQPCT
          .GGD....A.STCENA.......V.P.PC.
Retrocopy RGGDEKNAATSTCENAVLGETSNVSPAPCS

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_1 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	Si032233m.g	1 retrocopy	retro_sita_1 ,