RetrogeneDB ID: retro_sita_26

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 1:42005654..42007331(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si016805m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si009748m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_26
ATGGGCAACTCGTGCCGCGGCTCCTTCACGCCCACCTACACATCCACGACGGCCGACGAGTACAAGCGCGGCAGCTCCCG
GTCCTTTGTCACGTCGTCGTCGGCCACCTCCCTCCTCTCGGCGGCGAGCAGCAGCAGCGCCGCAGCAGGTAGCCGTGCGG
TCGGCAGCATGCGCGGCGGTCACCAGCAGCAGCTGTCGTCCCCCACGGCCGTGCTGGGGCACGCCACGCCGCCGCTGCGC
GAGCTCTACGCCGTGGGGCGCAAGCTCGGGCAGGGCCAGTTCGGCACCACCTACCTGTGCACGGAGCTCGCCACCGGCAC
CGCGCTGGCCTGCAAGTCCATCGCCAAGCGCAAGCTGCTCACCCCTGAGGACGTCGACGACGTCCGCCGCGAGATCCATA
TCATGCACCACCTCGCCGGCCACGCCAGCGTCGTCACCATCAAGGGCGCCTACGAGGACCCGCTCTACGTCCACATCGTC
ATGGAGCTCTGCGAGGGTGGCGAGCTCTTCGACCGCATCGTCGACCGCGGCTACTTCTCCGAGCGCAAGGCCGCCGAGAT
CGCGCGCGTCATCGTCGGCGTCGTCGAGGCCTGCCACTCCCTCGGGGTCATGCACCGGGACCTCAAGCCCGAGAACTTCC
TGCTGCTCAAGAACAACGACGGCAAGGACGGCGACGGCGACGAGGCGGAGCTCAAGGCCATCGACTTCGGCCTCTCCGTC
TTCTTTAAGCCGGGGCAGGTCTTCACCGACGTCGTGGGCTCCCCCTACTACGTCGCCCCCGAGGTGCTCTGCAAGCACTA
CGGCCCCGAGGCCGACGTGTGGACGGCGGGGGTCATCATCTACATCCTCCTCAGCGGGGTGCCGCCCTTCTGGGCCGAGA
CGCAGCAGGGCATCTTCGACGCCGTCCTCCGGGGTACCATCGACTTCGACTCCGAGCCATGGCCCGCCATCTCCGACAGC
GCCAAAGACCTCATCCGCCGCATGCTGCGCTCGCCCCCCGCCGAACGCCTCACCGCGCACCAGGTCCTCTGCCACCCGTG
GATCTGCGAGAACGGCGTCGCCCCGGACAGGCCCCTCGACCCCGCCGTCCTCTCCAGGCTCAAGCACTTCTCCGCCATGA
ACCGCCTCAAGAAGATGGCGCTCCGGGTCATCGCCCAGAGCCTCTCCGACGAGGAGCTCGCGGGGCTCAAGGAGATGTTC
AAGGCCATGGACACAGACGCCAGCGGCGCCATCACCTTCGACGAGCTCAAGGAGGGCCTGCGCCGCCACGGCTCCAACCT
GCGCGAGAGCGAGGTCCGGGACCTCATGGACGCCGCCGACGTCGACCGCAGCGGCACCATCGACTACGACGAGTTCATCG
CCGCCACCGTCCACATGAGCAAGCTCGACCGCGAGGAGCACCTGCTCGCCGCGTTCGCCTACTTCGACAAGGACGGCAGC
GGTTACATCACCGTCGACGAGCTCGAGCAGGCCTGCAGGGACCACAACATGGCCGACGTCGGCATCGACGACATCATCAG
GGAGGTCGACCAGGACAACGACGGCCGCATCGACTACGGCGAGTTCGTCGCAATGATGAAGAAGGGCATCATCGGGCACG
GCAGGCTCACAATGAGGCACAACTCCGACGGCAGCGTCCTGCACGGCGCCTGCACAACCATGGATCCATGTCTTTAA

Alignment

ORF - retro_sita_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 56.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDLSLKAIDFGLSVFFKPGQVFTDVVGSPYYVAPEVLCKNYGPAADVWTAGVILYILLSGVPPFWAETQQ
          D...LKAIDFGLSVFFKPGQVFTDVVGSPYYVAPEVLCK.YGP.ADVWTAGVI.YILLSGVPPFWAETQQ
Retrocopy DEAELKAIDFGLSVFFKPGQVFTDVVGSPYYVAPEVLCKHYGPEADVWTAGVIIYILLSGVPPFWAETQQ

Parental  GIFDAVLKGVIDFDSDPWPVISDSAKDLIRRMLNPRPAERLTAHEVLCHPWIRDHGVAPDRPLDPAVLSR
          GIFDAVL.G.IDFDS.PWP.ISDSAKDLIRRML...PAERLTAH.VLCHPWI...GVAPDRPLDPAVLSR
Retrocopy GIFDAVLRGTIDFDSEPWPAISDSAKDLIRRMLRSPPAERLTAHQVLCHPWICENGVAPDRPLDPAVLSR

Parental  IKQFSAMNKLKKMALRVIAESLSEEEIAGLKEMFQTMDTDNSGAITYDELKEGLRKYGSTLKDTEIRDLM
          .K.FSAMN.LKKMALRVIA.SLS.EE.AGLKEMF..MDTD.SGAIT.DELKEGLR..GS.L...E.RDLM
Retrocopy LKHFSAMNRLKKMALRVIAQSLSDEELAGLKEMFKAMDTDASGAITFDELKEGLRRHGSNLRESEVRDLM

Parental  DAADIDNSGTIDYIEFIAATLHLNKLEREEHLVAAFSYFDKDGSGYITVDELQQACKEHNMPDAFLDDVI
          DAAD.D.SGTIDY.EFIAAT.H..KL.REEHL.AAF.YFDKDGSGYITVDEL.QAC..HNM.D...DD.I
Retrocopy DAADVDRSGTIDYDEFIAATVHMSKLDREEHLLAAFAYFDKDGSGYITVDELEQACRDHNMADVGIDDII

Parental  NEADQDNDGRIDYGEFVAMMTKGNMGVGRRTMRNS
          .E.DQDNDGRIDYGEFVAMM.KG..G.GR.TMR..
Retrocopy REVDQDNDGRIDYGEFVAMMKKGIIGHGRLTMRHN

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_26 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Setaria italica	Si009748m.g	1 retrocopy	retro_sita_26 ,