RetrogeneDB ID: retro_sita_21

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 5:5615537..5616608(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si002017m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si008259m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_21
ATGGCGGCGACGGCGGCGAACCGGCGCGTGATCCTCAAGGACTACGTGGAGGGGTACCCCCGGGAGGAGCACATGGAGGT
GCTCCCTGGCGCCGAGGTGCCCCTCCGCCTCGCCGGCGACGACCCGCCCGGGTCCGTCCTCGTCCGCAACCTCTACCTCT
CCTGCGACCCCTACATGCGGCCCAAGATGTCGCGCCCGCTGCGGGAGTCCTACACGGCCGCCTTCACCCCGGGCTCCGTC
ATCACGGGCTACGGCGTCGCCCGCGTGCTCGACTCCTCCGACCCGCGCCTCGCGCCCGGGGACCTCGTATGGGGCATCAC
CGGCTGGGAGGACTACAGCGTCGTCAAGCCCCCCGCCACCGCCTTCCTCGCCAAGATCTCCCACGGCGGCGAGGGCGGGG
GCGTCCCGCTGTCCTACTACACCGGCATCCTCGGCATGCCGGGCCTCACCGCCTACGTGGGGTTCCACGAGATCTGCGCG
CCGAAGAAGGGCGAGACCGTCTTCGTCTCCGCGGCCTCCGGCGCCGTGGGCCAGCTGGTGGGCCAGTTCGCGCGGCTCGC
CGGGTGCCACGTCGTCGGCAGCGCGGGGTCTAAGGAGAAGGTGGAGCTCCTCAAGACGAAATTCGGGTTCCACGACGCCT
TCAACTACAAGGAGGAGGCCGACCTCGCCGCCGCGCTCAAGCGGTGCTTCCCGGAGGGCATCGACATCTACTTTGAGAAC
GTGGGCGGCGCCATGCTCGACGCCGTGCTGCTCAACATGCGCGTCCACGGCCGCATCGCCGTCTGCGGGTTCATCTCGCA
GTACAACCTGAGGGAAGGGGAGAAGGACGCCGTGCGCAACCTCTCCGCCGTCATCGGCAAGCGGCTCCGGATGCAGGGGT
TCATCGAGCCCGACCACAAGCACCTGTACCCGCAGTACGAGGCGTGGGTGCTGCCATACATCAGGGACGGCACCATCGCC
TACGTCGAGGACGTCGCCGAGGGCCTCGAGAGCGCGCCCAAGGCGCTCATCGGCCTCTTCCACGGCCGCAACGTCGGCAA
GCAGCTCGTCCGCATCGCCGACGACGAATGA

Alignment

ORF - retro_sita_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.43 %
• Parental protein coverage: 89.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GEVLVRNLYLSIDPYQLNRMKRSSASHLAVDGILPGQRIAAYAAGEVVASASPEYAAGDVVAGVLGWEDY
          G.VLVRNLYLS.DPY....M.R............PG..I..Y....V..S..P..A.GD.V.G..GWEDY
Retrocopy GSVLVRNLYLSCDPYMRPKMSRPLRESYTA-AFTPGSVITGYGVARVLDSSDPRLAPGDLVWGITGWEDY

Parental  TLFTPSPAVLMSKVDASASASAAAGGFPLSHHISALGTSGMTAYGGLFEVCRPAKGDKVFVSAASGSVGS
          ....P.......K.....S.....GG.PLS.....LG..G.TAY.G..E.C.P.KG..VFVSAASG.VG.
Retrocopy SVVKPPATAFLAKI----SHGGEGGGVPLSYYTGILGMPGLTAYVGFHEICAPKKGETVFVSAASGAVGQ

Parental  LVGQFAKLAGCYVVGCAGTKAKVDLLKDKLGFDDAFNYKEEPDLNAALKRYFPDGIDIYFENVGGEMLEA
          LVGQFA.LAGC.VVG.AG.K.KV.LLK.K.GF.DAFNYKEE.DL.AALKR.FP.GIDIYFENVGG.ML.A
Retrocopy LVGQFARLAGCHVVGSAGSKEKVELLKTKFGFHDAFNYKEEADLAAALKRCFPEGIDIYFENVGGAMLDA

Parental  ALANMNTHGRVAVSGVISEYT--GAGRRAAPDLMEVIYKRITIRGFLAWDFLPRFAEFNAIIGEWIREGK
          .L.NM..HGR.AV.G.IS.Y........A...L..VI.KR....GF...D.........A.....IR.G.
Retrocopy VLLNMRVHGRIAVCGFISQYNLREGEKDAVRNLSAVIGKRLRMQGFIEPDHKHLYPQYEAWVLPYIRDGT

Parental  VQVVEDVSDGLESVPSAFAALFQGQNVGKKLVKLA
          ...VEDV..GLES.P.A...LF.G.NVGK.LV..A
Retrocopy IAYVEDVAEGLESAPKALIGLFHGRNVGKQLVRIA

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_21 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
Zea mays	GRMZM2G019872	1 retrocopy	retro_zmay_10,
Setaria italica	Si008259m.g	1 retrocopy	retro_sita_21 ,