RetrogeneDB ID: retro_sita_27

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 5:44283336..44284458(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si001896m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si026545m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_27
ATGGCGCAGGTGGCTAAGCGGCTTCTCCTGGTGGCCCTGTTGGTGGTGTCAGCGGTGGAGCTGTGCCGCGCCATGCCGTT
TGACAAGAAGGACCTGGAGTCGGACGAGGCGCTGTGGGACCTGTACGAGCGGTGGCAGGCGCACCACCGCGTGCACCGGC
ACCACGGCGAGAAGGGCCGCCGCTTCGGCACCTTCAAGGAGAACGTCCGCTTCATCCACGCCCACAACACGCGCGGCGAC
CGCCCCCACTACCGCCTCCGCCTGAACCGCTTCGGCGACATGGGCCGCGAGGAGTTCCGCTCCGCGTTCGCCGACTCCCG
CATCAACGACCTCCGCCGGGAGCCCCACGCCGCGGCCGCGGTGCCCGGGTTCATGTACGAGGACGTCGCCTACCTGCCGA
GCTCCGTGGACTGGCGCCAGGAGGGCGCGGTCACCGCCGTCAAGAACCAGGGCAAGTGCGGCAGCTGCTGGGCCTTCTCC
ACGGTGGTGGCCGTGGAGGGCATCAACGCGATCCGGACGGGGAGGCTGGTGTCTCTGTCGGAGCAGGAGCTGATCGACTG
CGACAAGGAGGAGAACGGGTGCCAGGGCGGGCTGATGGAGAACGCCTTCGAGTTCATCAAGGCCCACGGCGGCATCACCA
CCGAGGCCACCTACCCGTACCGCGCCCGCAACGGCACCTGCGACAGCTACCGATCCCGGCGCGGGCAGCTGGTGTCCATC
GACGGGCACCAGATGGTCCCGGCGGGTAACGAGGAGGCCCTGGCCAAGGCGGTGGCGAACCAGCCGGTGTCCGTGGCCAT
CGACGCCGGGGGCCAGGCGTTCCAGTTCTACTCGGAGGGCGTGTTCACGGGGGACTGCGGCACGGACCTGGACCACGGCG
TGGCGGCGGTCGGGTACGGCGTCGGCGACGACGGCACGCCGTACTGGGTCGTGAAGAACTCCTGGGGCCCCGGGTGGGGC
GAGGGCGGGTACATCCGGATGCAGCGCGGCGCCGGCGACGGCGGGCTCTGCGGCATCGCCATGGAGGCATCCTTCCCCAT
CAAGACGTCCCCCAACCCGGTGCGCAAGCCCCGGCGCGCGCTCCTCTCCGGGGACGCCTCCGTCTCCACCTCGTCCCAGT
GA

Alignment

ORF - retro_sita_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.51 %
• Parental protein coverage: 80.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DKARRFNVFKENVRYIHEANKK-DRP-FRLALNKFADMTTDEFRRTYAGSRVRHHRALSGGRRAEGSFMY
          .K.RRF..FKENVR.IH..N...DRP..RL.LN.F.DM...EFR...A.SR....R.......A...FMY
Retrocopy EKGRRFGTFKENVRFIHAHNTRGDRPHYRLRLNRFGDMGREEFRSAFADSRINDLRREPHAAAAVPGFMY

Parental  ADAGSLPPAVDWRQRGAVTGIKDQGQCGSCWAFSTIAAVEGINKIRTGKLVSLSEQELVDCDDGDNQGCN
          .D...LP..VDWRQ.GAVT..K.QG.CGSCWAFST..AVEGIN.IRTG.LVSLSEQEL.DCD...N.GC.
Retrocopy EDVAYLPSSVDWRQEGAVTAVKNQGKCGSCWAFSTVVAVEGINAIRTGRLVSLSEQELIDCDKEEN-GCQ

Parental  GGLMDYAFQYIKRNGGITTESNYPYLAEQRGCNRAKERSHD-VTIDGYEDVPANNEDALQKAVANQPVAV
          GGLM..AF..IK..GGITTE..YPY.A....C.....R....V.IDG...VPA.NE.AL.KAVANQPV.V
Retrocopy GGLMENAFEFIKAHGGITTEATYPYRARNGTCDSYRSRRGQLVSIDGHQMVPAGNEEALAKAVANQPVSV

Parental  AIDASGQDFQFYSEGVFTGSCGTDLDHGVAAVGYGITRDGTKYWIVKNSWGEDWGQRGYIRMQRGVSDSQ
          AIDA.GQ.FQFYSEGVFTG.CGTDLDHGVAAVGYG...DGT.YW.VKNSWG..WG..GYIRMQRG..D..
Retrocopy AIDAGGQAFQFYSEGVFTGDCGTDLDHGVAAVGYGVGDDGTPYWVVKNSWGPGWGEGGYIRMQRGAGDG-

Parental  GLCGIAMEPSYPTKSA
          GLCGIAME.S.P.K..
Retrocopy GLCGIAMEASFPIKTS

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_27 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G19707	2 retrocopies	retro_bdis_26, retro_bdis_41,
Zea mays	GRMZM2G099765	1 retrocopy	retro_zmay_16,
Hordeum vulgare	MLOC_73076	2 retrocopies	retro_hvul_23, retro_hvul_68,
Oryza barthii	OBART11G08490	1 retrocopy	retro_obar_27,
Oryza glumaepatula	OGLUM05G09560	1 retrocopy	retro_oglu_31,
Oryza meridionalis	OMERI11G07520	1 retrocopy	retro_omer_2,
Setaria italica	Si026545m.g	1 retrocopy	retro_sita_27 ,