RetrogeneDB ID: retro_sita_40

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 1:28923320..28925051(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si019482m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si003861m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_40
ATGGGCCAAGTTGAGTCGTCGGCCGCTAGCTACGGCTGGTGGCGGTGCCTCCTCGTCGTGCCGGTGCTCTATTCGGCGTG
GGCGTCGCCGTTCGAGCTGGCCGTGGAGAGGGCCGCCACCCTGCCACTCCTCGTCGTCGATCTGGTAGCCGACGCGTTCT
TTGCCGTCGACATCGCCGCTTCCATCCTCGCTGCGTGCCGACGCCTCCGCGGCACCACCGGCATCTTCGTCGACGACCGC
AAGAAGGCCGCCGTCAGGCACCTGCGCCCGTGGACGTTCGCGATGGACGCGGCCTCCACGGTCCCGTTCCAGGCCATTTA
CCACCTGGCGGCCGGCCGGGGCGCCGCCGCATGGTCGTCGCCGTGCCGGTTCCTGAGCCTCCTCCGGCTGTGGCGTCTGC
GGCGCGTCAGCGAGCTCTTCGCGAGGCTGGAGAAGGACGTCCGTCTAAACTACTTCTGGACCAGGCTCGTCAGGCTCGCC
GGCGTGACGCTCCTCGCCGTGCACGCCACCGCGTGCGCCCACCTGTGGATGGCATCCCACTACCGCGGACCCACGTGGCT
CGGCCGGGGCTTCGAGTCCCGCAGCGTCTGGGCCGGGTACGTCCGCGCCGCCTACTGGTCCGTCGCCACGCTCACCACCG
TCGGCTACGGCGACCTGCACCCGGCCAACCCCGGCGAGATGGCGTTCGCCGTCCTCCTCGTGCTCTTCAACCTCGGCCTC
GCCGCGTATGTCGTCGGCAACATGACCAACCTCGTCGCCGCCGCCTCCGCGCCCGCCCTCGCGCTGCGGGACACGCTGCT
CGGGGTCTCCGCGTTCGGGGCCAAGAACCGGCTGCCGGAGGCGCTGACGGAGCAGATCGCGGAAATCGTGCAGCTCAACT
TCGACACCACGGAGCAGCTGCTCCAGCCGGAGCTCCTGTCCGAGATGCCTAGGGCGGTGCGGTCGGAGATCGCGCAGCAC
CTGTTCCGGGACACCGTCGAGGGCGCCTACCTGTTCCGTGGCGTCTCCGAGGGCCTCGTCGTCGACCTCGTCTCCGACAT
GACGACGGCGCAGTTCTTCCCTCCCAAGGCCGACATCGTCCAGCAGGGCGAGAACCCCACGGACTGCTACATCATCGTGT
CCGGCTCCGTAGACGTGCTGGCGGCCGCCACCGACGGCACGGAGACGGTCGTGTCGAAGGCGGGGCCGCGCGGCATGGCG
GGGGAGATCGGCGTGGTGCTCAACACCCAGCAGCCGTTCACCGTCCGGTGCCGGAGGCTGACTCAGGTCGTGCGCGTCAG
CCAGAGCCACCTTCTCCGGGCACTCCGGCCGCACGCCGCCGACGCTGACAGGCTGTTCTGCAACTTCGTTCAGCACCTTG
AATCTCCCGTGTGGCAAGTTGCGAGGAAGGAAGCGCCATTCCTCAGGGAGGCCTCAGCTCAGCTTCGGGCGGGTGCCGCC
GCCGCCGCCGCGACGTCGAGCCGGAGGAGCGAGATGATGGACGGTGCGCGGCTGGAAGAGGCTGATCGGAGAACGTCGCG
GCGGAGAGAGCCCATCAAGCGAGTGGTTATCCATCCGAAGTCTGCAAATAAGACAGGGAAGCTCGTACGCCTTCATGGTT
CGATGCAAGAGCTGATGAGGGTTGCGGAGGCGAAGTTCGGGAAGGCGGTGACGACGGTGCTCACCGTCGACGGCGCCGAA
GTTGAGGACGTCGACGTGCTAAGAGATGGAGATCACTTGTTCTTATGCTAG

Alignment

ORF - retro_sita_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.9 %
• Parental protein coverage: 55.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STGFRYLNLLRLWRLRRVSKLFARWEKDIRFNYFYTRLVKLIGVTLFALHSSACIFLWMAFHHRDKEHTW
          S...R.L.LLRLWRLRRVS.LFAR.EKD.R.NYF.TRLV.L.GVTL.A.H..AC..LWMA.H.R....TW
Retrocopy SSPCRFLSLLRLWRLRRVSELFARLEKDVRLNYFWTRLVRLAGVTLLAVHATACAHLWMASHYRGP--TW

Parental  LGSQVRDFTDRSVWVGYTYAVYWSITTLATVGYGDLHAVNPGEMAFATGYMLFNLGLTSYIIGNMTNLVV
          LG...R.F..RSVW.GY..A.YWS..TL.TVGYGDLH..NPGEMAFA....LFNLGL..Y..GNMTNLV.
Retrocopy LG---RGFESRSVWAGYVRAAYWSVATLTTVGYGDLHPANPGEMAFAVLLVLFNLGLAAYVVGNMTNLVA

Parental  HAATNTFRMRDMVRRVSTFGAANQLPRELREQMMASAQLRFNAGE-VVQQQLLSDLPRALRSGVAQHLFG
          .A.......RD....VS.FGA.N.LP..L.EQ.....QL.F...E...Q..LLS..PRA.RS..AQHLF.
Retrocopy AASAPALALRDTLLGVSAFGAKNRLPEALTEQIAEIVQLNFDTTEQLLQPELLSEMPRAVRSEIAQHLFR

Parental  DTVQRCYLFQGVSSGLVVQLVSEMV-AGYFPPKADIVLQNETSTDCYIVVSGAVDVLATADDGTEKLVMK
          DTV...YLF.GVS.GLVV.LVS.M..A..FPPKADIV.Q.E..TDCYI.VSG.VDVLA.A.DGTE..V.K
Retrocopy DTVEGAYLFRGVSEGLVVDLVSDMTTAQFFPPKADIVQQGENPTDCYIIVSGSVDVLAAATDGTETVVSK

Parental  VGPHGMAGEMGVIFGTPQPFTVRSRRLTQVVRISRSHLLQILRPNTADADTVHANFVQYLRSLREHVA-V
          .GP.GMAGE.GV...T.QPFTVR.RRLTQVVR.S.SHLL..LRP..ADAD....NFVQ.L.S....VA..
Retrocopy AGPRGMAGEIGVVLNTQQPFTVRCRRLTQVVRVSQSHLLRALRPHAADADRLFCNFVQHLESPVWQVARK

Parental  DAPFFRE
          .APF.RE
Retrocopy EAPFLRE

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_40 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004342	1 retrocopy	retro_oind_32,
Oryza brachyantha	OB01G37960	1 retrocopy	retro_obra_2,
Oryza barthii	OBART01G29050	1 retrocopy	retro_obar_20,
Oryza glumaepatula	OGLUM01G33050	1 retrocopy	retro_oglu_27,
Oryza nivara	ONIVA01G33130	1 retrocopy	retro_oniv_11,
Oryza rufipogon	ORUFI01G32100	1 retrocopy	retro_oruf_17,
Oryza sativa japonica	OS01G0718700	1 retrocopy	retro_osat_1,
Setaria italica	Si003861m.g	1 retrocopy	retro_sita_40 ,