RetrogeneDB ID: retro_sita_49

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 4:5023789..5023993(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si007595m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_49
CCGAGGAAGGCGCGGAGGAAGCTCGGCACGGCCTTCCGCTGCCCGGTCTGCAAGCGCGCCGAGAGCGTGGAGTGCCGGAT
CGACCCCAAGCGCAAGGTCGCCGAGGCCTCGTGCTGCGGCTGCGAGGCGAGCTACTCCACCGCCGCCGACGCGCTGACCG
AGCCCATCGACGTCTACTGCGAGTGGGTCGACGAGCGCAGCCGT

Alignment

ORF - retro_sita_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.41 %
• Parental protein coverage: 76.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKKRMDKLDTVFSCPFCNHGSSVECRIDMKNLIGEASCRICQENFSTTVNALTEPIDIYSEWIDECER
          P.K...KL.T.F.CP.C....SVECRID.K....EASC..C....ST...ALTEPID.Y.EW.DE..R
Retrocopy PRKARRKLGTAFRCPVCKRAESVECRIDPKRKVAEASCCGCEASYSTAADALTEPIDVYCEWVDERSR

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_49 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA007878	1 retrocopy	retro_oind_10,
Aegilops tauschii	F775_28085	1 retrocopy	retro_atau_24,
Hordeum vulgare	MLOC_14907	3 retrocopies	retro_hvul_85, retro_hvul_89, retro_hvul_97,
Oryza barthii	OBART07G23140	1 retrocopy	retro_obar_9,
Oryza glumaepatula	OGLUM07G23200	1 retrocopy	retro_oglu_13,
Oryza nivara	ONIVA07G23000	1 retrocopy	retro_oniv_49,
Oryza sativa japonica	OS07G0631100	1 retrocopy	retro_osat_82,
Sorghum bicolor	Sb10g003710	1 retrocopy	retro_sbic_12,
Setaria italica	Si007595m.g	2 retrocopies	retro_sita_49 , retro_sita_50,
Triticum aestivum	Traes_1DL_84C83461E	2 retrocopies	retro_taes_162, retro_taes_71,