RetrogeneDB ID: retro_sita_2

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: scaffold_11:97012..98011(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si020698m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si002089m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_2
ATGGCTTCCCAGCTGATGTTCCGTGGCAGCAGGTTCTTGTTGTTGGTGCTCGTCGTGGCGTCGTCGACCCTGATGATGGA
CACAACAACGGCGCAGCTGCAGTACGATTTCTACAACACGACGTGCCCGGGCGTGGAGGACCTGGTGCGCGCCGAGCTGC
TGGCCCTGTTCGCCGCCGACGTCACGCTCCCGGCGGGTCTCCTCCGGCTGCACTTCCACGACTGCTTCGGCGCCGGCTGC
GACGCCGCGCTCCTGCTAAAGTCGCACAACGGCACGGCCCAGCGCGACGCCGACCCCAACTCCACGGTGCGCGGCTACGA
GGCCATCGAGGCCGTCAAGGCCAAGGTCGAGGAGGCCTGCCCGCTCGTCGTCTCCTGCGCCGACATCATGGCGATGGCGG
CGCGAGACGCGGTCAACTACACCCAGGGCCCTGCGTACGCGGTGGAGACCGGGCGGCGCGACGGCAACGTCTCCCGCAAG
GAGGACGCCCTGCGCTTCCTGCCTCCCGCCGACGGCAACGTCACCGTCCTCACCCAGTACTTTGCCGCCCAGAACCTCAG
CTACAAGGACATGGTCGTCCTCTCCGCCGCCCACTCCATCGGTGTCGCGCACTGCCCCTCCTTCTCCAACCGCCTCTACA
ACTACACCGGCGCCGGCGACCAGGACCCATCGCTCGACGCCGACTACGCCAAGAACCTCACGGCGAAGTGCAAGCCGGGC
AACGTCGCCACCGTGCAACCGCTCGACCCCACGACGCCCAGCACCTTCGACCTGGGGTACTACAACAACGTCTACAACCA
CCGGGCGCTGCTCGCCTCCGACGCCGCGCTGCTCAACGACAGCCTCTCCGGCGCCTACGTCCAACTCATGACCAACGCCT
CCTCCGTCGACGTCTTCTTCGCCGACTTCGCCGTCTCCATGATCAACATGGGAAGGATCGGAGTGCGCACCGGCACCGAC
GGCGAGATCAGGGCCACATGCGCAATCTACGTCGACTGA

Alignment

ORF - retro_sita_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.1 %
• Parental protein coverage: 88.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGLAVGFYNASCPEVEDLVLAEMRAIVAKDRTLGPALLRFMFHDCLVRGCDASIMLESRSKKGEQDAVPS
          A.L...FYN..CP.VEDLV.AE..A..A.D.TL...LLR..FHDC...GCDA...L.S.......DA.P.
Retrocopy AQLQYDFYNTTCPGVEDLVRAELLALFAADVTLPAGLLRLHFHDCFGAGCDAALLLKSHNGTAQRDADPN

Parental  YGLRGYEEVERIKAKVEEACPLTVSCADIIALAARDAVYLSNGPRYAVETGRRDGKVSAKSDADNDLPPP
          ...RGYE..E..KAKVEEACPL.VSCADI.A.AARDAV....GP.YAVETGRRDG.VS.K.DA...LPP.
Retrocopy STVRGYEAIEAVKAKVEEACPLVVSCADIMAMAARDAVNYTQGPAYAVETGRRDGNVSRKEDALRFLPPA

Parental  FSNIVDLKTYFSVKGLGWKDLVVLSGSHTIGSAQCSSFASDRLYNYSGRGVQDPSLNKTFAAGLREACEA
          ..N...L..YF....L..KD.VVLS..H.IG.A.C.SF.S.RLYNY.G.G.QDPSL....A..L...C..
Retrocopy DGNVTVLTQYFAAQNLSYKDMVVLSAAHSIGVAHCPSF-SNRLYNYTGAGDQDPSLDADYAKNLTAKCKP

Parental  GRENDTTPVYMDSTTPYDFDLGYYRDVLSNTSLFLSDKALMDDRWTRTYVERMAAAASPDEFFDDYAVAM
          G..N..T....D.TTP..FDLGYY..V.....L..SD.AL..D.....YV..M..A.S.D.FF.D.AV.M
Retrocopy G--NVATVQPLDPTTPSTFDLGYYNNVYNHRALLASDAALLNDSLSGAYVQLMTNASSVDVFFADFAVSM

Parental  TNMGRLEVLTGDNGEIRKTCTSYVD
          .NMGR..V.TG..GEIR.TC..YVD
Retrocopy INMGRIGVRTGTDGEIRATCAIYVD

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_2 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Setaria italica	Si002089m.g	1 retrocopy	retro_sita_2 ,