RetrogeneDB ID: retro_sita_14

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 2:26790077..26791208(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si030198m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si036015m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_14
ATGTCGATGGCGCAGGTGTGCTGCGACTCGGCGGCCGCAGCGGTGGCGGCGGCGGTGGCTGGGCCGGAGGCGGAGGCCCG
GGCGAGGGCGCGCGCCGAGAGGAGGCGTCGGGCAGGGGAGGCCGGGAGGTGGAAGCACGCCGCCGCGGCGGCGGCGGTGG
CGCCTGGGTCGGCCGAGGCCGTCGCGGCCACGAGGAAGCGCCGCGTCGACGCGGGGGAGCTGCTCGTGGCGCGGAAGCAC
GGGGCGGCCTCGGTGGCCGGCCGCAGGAGGGAGATGGAGGACGCCGTGTCCGTGCGCGAGGCGTTCGTCGCGCCCTCCGC
TGCTGTGGACGAGGGGCGCCCCGCCGTCGGGAGCGGGAGGTGCGATTTCTACGGGGTGTTCGACGGCCACGGCTGCTCCC
ACGTCGCCGAGGCGTGCCGGGACCGGATGCACGACCTGCTCGCCGAGGAGCTGTCCACCGGCGGCGACGGGGCGGCGCTG
CCGCGGGAGCCCGCGGCCTGGACCGAGGCGATGGAGCGGTGCTTCGCGCGGATGGACGCCGAGGTGGCCTCCGCCGGTGG
TCGCGCCGCGGCGACCGCCAGCGCCAGCTGCCGCTGCGACGCGCACAAGCGCGACCACGTGGGCTCCACGGCCGTGGTGG
CCGTCGTGGAGGAGCGCCGGGTGGTGGTCGCCCACTGCGGCGACTCCCGCGCGGTGCTCTGCCGCGGCGGCGGCGGCGCG
GCGCCGGTGCCGCTGTCCTCGGACCACAAGCCCGACCGGCCCGACGAGCAGGAGCGGATCGAGTCCGCGGGCGGGCGCGT
CATCTTCTGGGAGGGCGCGCGGGTGCTGGGCGTGCTGGCCATGTCCCGCGCCATCGGGGACGGGTACCTCAAGCCGTACG
TGTCGTCGGTGCCCGAGGTGACGGTGACGGACCTCGTCGAGGACGACGAGTGCCTCATCCTGGCCAGCGACGGGCTGTGG
GACGTGGTGAGCAACGAGGCCGCCTGCGAGGTGGCGCGCGCCTGCCTCCGCAGGGGCAGGGAGAAGTGGTGCGCCGAGGC
CGCCGCGCTGCTCACCAAGCTGGCCCTCGCCAGGCGCAGCGCCGACAACGTCTCCGTCGTCGTCGTCGACCTCCGCCGGA
AGAACCACTAG

Alignment

ORF - retro_sita_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.18 %
• Parental protein coverage: 54.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FFGVFDGHGCSHVATSCGVRMHEIVAEEAAAAAAGSSASDEAARWRDVMEKSYARMDAE--AVGSRDTTG
          F.GVFDGHGCSHVA..C..RMH...AEE......G.....E.A.W...ME...ARMDAE....G.R....
Retrocopy FYGVFDGHGCSHVAEACRDRMHDLLAEELSTGGDGAALPREPAAWTEAMERCFARMDAEVASAGGRAAAT

Parental  PAPTCRCEMQMPKCDHVGSTAVVAVVGPRHLVVANCGDSRAVLCSGG---AAIPLSADHKPDRPDELERI
          ....CRC.....K.DHVGSTAVVAVV..R..VVA.CGDSRAVLC.GG...A..PLS.DHKPDRPDE.ERI
Retrocopy ASASCRCDAH--KRDHVGSTAVVAVVEERRVVVAHCGDSRAVLCRGGGGAAPVPLSSDHKPDRPDEQERI

Parental  HAAGGRVIFWDGARVFGMLAMSRAIGDSYLKPFVISDPEVRVVERKDGEDEFLILASDGLWDVVSNEVAC
          ..AGGRVIFW.GARV.G.LAMSRAIGD.YLKP.V.S.PEV.V.......DE.LILASDGLWDVVSNE.AC
Retrocopy ESAGGRVIFWEGARVLGVLAMSRAIGDGYLKPYVSSVPEVTVTDLVE-DDECLILASDGLWDVVSNEAAC

Parental  KVVRACLRNG
          .V.RACLR.G
Retrocopy EVARACLRRG

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_14 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_56081	1 retrocopy	retro_hvul_16,
Oryza punctata	OPUNC03G11550	1 retrocopy	retro_opun_31,
Oryza sativa japonica	OS03G0268600	1 retrocopy	retro_osat_49,
Sorghum bicolor	Sb01g039890	1 retrocopy	retro_sbic_41,
Setaria italica	Si036015m.g	1 retrocopy	retro_sita_14 ,