RetrogeneDB ID: retro_sita_15

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 3:45065767..45066925(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si022320m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si010340m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_15
ATGTCCACGGCGGAGGAAGCCGCCGGTGCCTTCGACCGACTGAGCGAGCTCAAGGCGTTCGACGACACCAAGGCCGGCGT
CAAGGGCCTCGTCGACGCCGGCATCACCGCCGTCCCCGCCATCTTCCGCCACCACCACCAGGGCCCCCTCGTATCCTCTG
TCAGCAGCAGCGGCAGCGGCGGCGGCGGCGCCATCAGCATCCCGGTCATCGACCTCTCGGCGTCTTCGTCATCGGACGCC
CGCGCCCGCGCGGAGGTGGTGGCCCAGGTTAAGGCCGCGGCGGAGACGGCCGGGCTCTTCCACCTTGTCAACCACGGCGT
CCCCGGCGAGCTCTTGTCTGATATGCTCGCCTCCGTGCGGCGGTTCCACGAGGCGCCACCGGAGGCGAAACGGCCGTACT
ACACCCGCGACCCCGGGCGCCGCCTCCGCTTCAACTCCAACTTCGACCTCTTCAGCTCGCCGGCGGCCAACTGGCGCGAC
ACCCTCTTCTGCGCCGCGGCGCCGGATCCCCCACCCCCGGAGGAGCTCCCGCCCGCCGTCCGCCACGTGATGCCCGAGTA
CGCCGCCGCCGCGCGCGGGGTGGCGGCGCGGGTGTTGGCGCTCCTGTCGGAGGCGCTGGGGCTCGCCGCCGGCCGCCTCG
CCGGGATGGGGTGCGCGGAGGGGCTCAGCCTGGTGTGCAACTACTACCCGCCGTGCCCGGAGCCGGAGCTCACCCTGGGG
TGCGGCGCGCACTCGGACCCCAGCTTCCTCACCGTGCTGCTGCGGGACGCGCACGATGAGGGGGGCCTGCAGGCGCGCCT
CGGCTGCGGCGGCGGAAGGTGGGTGGACGTGCCCCCCGTCGCCCCCTGCGCCCTCCTGGTGATCGTCGGTGACCTCCTCC
AGCTCGTCAGCAACGGGCGGTTCAGGAGCGCGGAGCACCGGGTGGTGGCCAGACGGAGCACGGACAAGGCGAGGGTGTCG
GTGGCATGCTTCTTCAACGCCGACGTCGCCAGGTCCACGAGGCTCTACGGGCCCATCGCCGAGCTCACGTCAGGCGGAAA
CGGCGACGACGGCGACGGCGCGCTGTACAGGAGCGTGACGGTGCCGGAGTTCCTGGCGCACTACGACAAGAAAGGCCTCG
ACGGCCGCCCGGCGCTCGACCACTTCCGGCTGCGATAG

Alignment

ORF - retro_sita_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.23 %
• Parental protein coverage: 87.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAAGVASGYDRRRELQAFDDTKAGVKGLVDAGVTAIPSIF-HHPPESLEDTTTSPPSCTDGAFAIPVVDL
          .A...A...DR..EL.AFDDTKAGVKGLVDAG.TA.P.IF.HH....L.....S..S...GA..IPV.DL
Retrocopy TAEEAAGAFDRLSELKAFDDTKAGVKGLVDAGITAVPAIFRHHHQGPLVSSVSSSGSGGGGAISIPVIDL

Parental  SA----DAR-REDVVAQVRHAAGTVGFFHVVNHGVPEGLMAGMLAGARRFNEGPAEAKRALYSRDQARKV
          SA....DAR.R..VVAQV..AA.T.G.FH.VNHGVP..L...MLA..RRF.E.P.EAKR..Y.RD..R..
Retrocopy SASSSSDARARAEVVAQVKAAAETAGLFHLVNHGVPGELLSDMLASVRRFHEAPPEAKRPYYTRDPGRRL

Parental  RFGSNFDLFQSAAANWRDTLFCDLAPDPPLPEELPEVLRNVIMEYGDAVMKLGLRVSELLSESLGLSSGH
          RF.SNFDLF.S.AANWRDTLFC..APDPP.PEELP...R.V..EY..A......RV..LLSE.LGL..G.
Retrocopy RFNSNFDLFSSPAANWRDTLFCAAAPDPPPPEELPPAVRHVMPEYAAAARGVAARVLALLSEALGLAAGR

Parental  LREMGCMESLHAVCQYYPPCPEPHLTFGIKSHTDPAFFTVLLQDG-STGGLQVLVDRGGGHRRTWVDVPP
          L..MGC.E.L..VC.YYPPCPEP.LT.G...H.DP.F.TVLL.D....GGLQ.....GGG....WVDVPP
Retrocopy LAGMGCAEGLSLVCNYYPPCPEPELTLGCGAHSDPSFLTVLLRDAHDEGGLQARLGCGGGR---WVDVPP

Parental  L-PGSLTVNIGDLLQLVSNDRFRSVEHRVPAIKSKDPARVSVASFFNTDLKRSTRLYGPITD
          ..P..L.V..GDLLQLVSN.RFRS.EHRV.A..S.D.ARVSVA.FFN.D..RSTRLYGPI..
Retrocopy VAPCALLVIVGDLLQLVSNGRFRSAEHRVVARRSTDKARVSVACFFNADVARSTRLYGPIAE

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_15 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	AC148152.3_FG005	1 retrocopy	retro_zmay_1,
Setaria italica	Si010340m.g	1 retrocopy	retro_sita_15 ,