RetrogeneDB ID: retro_sita_34

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 6:171927..172641(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si014375m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si010957m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_34
ATGGACATCAACAAGGCAGCAGGGGCCTCGCCGGCGGCCGTCGACGCGCGCACGGTGGTGGCGCACGTCCTGGCCGTGGC
CGCCACCGTGCTGGTGCTGGTCTGGTGCGTCCACTTCCGCGGCGGTCTGGCCCTCCGGTCCCAGGACAAGCAGCTCATCT
TCAACGTCCACCCCGTGCTCATGCTCCTGGGCCCCATCGTCCTCGCCGGAGAGGCCATCCTCTGCTACCGCTCCCTCCCG
CTCCTCAGCCGCGGCGCCAGGAAGAAGGCGCACCTGGCGCTGCACGCCGCGGGCCTCGGCGCCGGCGTCCTCGGTGTCTA
CGCCGTCTTCAAGTTCCACGTCGAGAGCGGCATCCCCAACCTCTACTCGCTCCACTCCTGGATCGGCATCGCCACCATCT
CCCTCTACGCGCTCCAGTGGGCCGCCGGCTTCCTCGCCTTCTTCTTCCCGGGCGCGTCGCCGGCCACACGGCGCAGGGCC
CTGCCGTGGCACGCCGTCGGCGGCCTCCTCGTCTTCGCGCTCGCCGTCGGCACCGCGCAGCTCGGCTTCCTCGAGAAGCT
CACCTTCCTGCAGGGCCCGCCGCTGCGCCTGCCCAGGCACGGCGCCGAGGCGCTGCTCGTCAACTTCACCGCGCTCGTCG
TGCTCCTACTCGGCGTCGCCGTCGTGCTCGCCACGGTCACCATGGACGCCACAAGGTACAACACCATCATGTAA

Alignment

ORF - retro_sita_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.68 %
• Parental protein coverage: 87.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TYAAHALAAVAAVLVLVWCVHFRGGLALEAPNKNLIFNVHPVLMLIGYIILGSEAIMIYKVFPNLNHDTA
          T..AH.LA..A.VLVLVWCVHFRGGLAL....K.LIFNVHPVLML.G.I.L..EAI..Y...P.L.....
Retrocopy TVVAHVLAVAATVLVLVWCVHFRGGLALRSQDKQLIFNVHPVLMLLGPIVLAGEAILCYRSLPLLSRGAR

Parental  KLTHLILHAIATVLGAFGIYCAFKFHNDSGIANLYSLHSWLGIGTISLYGIQWVFGFVTFFFPGAAPSLR
          K..HL.LHA.....G..G.Y..FKFH..SGI.NLYSLHSW.GI.TISLY..QW..GF..FFFPGA.P..R
Retrocopy KKAHLALHAAGLGAGVLGVYAVFKFHVESGIPNLYSLHSWIGIATISLYALQWAAGFLAFFFPGASPATR

Parental  RSALPWHALFGLFVYVLAVMTAELGFLEKLTFLESG--GLDKYGAEAFLVNFTALVVVLFGASVVVAAV
          R.ALPWHA..GL.V..LAV.TA.LGFLEKLTFL......L...GAEA.LVNFTALVV.L.G..VV.A.V
Retrocopy RRALPWHAVGGLLVFALAVGTAQLGFLEKLTFLQGPPLRLPRHGAEALLVNFTALVVLLLGVAVVLATV

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_34 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G034668	1 retrocopy	retro_zmay_23,
Leersia perrieri	LPERR04G16060	1 retrocopy	retro_lper_17,
Hordeum vulgare	MLOC_12641	1 retrocopy	retro_hvul_22,
Oryza sativa japonica	OS04G0533500	1 retrocopy	retro_osat_39,
Physcomitrella patens	PP1S194_18V6	1 retrocopy	retro_ppat_14,
Sorghum bicolor	Sb06g023650	1 retrocopy	retro_sbic_21,
Setaria italica	Si010957m.g	1 retrocopy	retro_sita_34 ,