RetrogeneDB ID: retro_sita_47

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 3:48588879..48590532(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si024562m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_47
ATGGCATCCCGGTTTTTCTTTCTTGTCGTTGCCGTCGTGGCCCGGCTCTGCAGCGCCGCTATGGCGACTGGTGGTCAGGC
CGACGACATCTTGCGGCCGTGGCCGCCTGACTGCTCGACGGCGGACAACTACACGGCCGACAGCCAGTACAAGAAGAACC
TGGACCAGCTCCTCGCCGCGCTCCCCGCGGCGGCCGGCGACAACGGCTGGTTCTACGAGGGCAGCGCCGGGGCCGGCACC
GACGACGAGGTGTTCGGCCTCATCATGTGCTACGCCGACCACAACGCGACGGCGTGCCTCGACTGCCTCTCCAGGGCGCC
CGCCGGGATCGCCACGGTGTGCCCGGGCAGCCGGAACGTTCGCGCCATGTACGACGCGTGCGTGCTCCGGTACTCGGCGG
CGCCGATCCCGGCCACCGCGGACCTCAGCTACTTGCACTCCGTGAACGGGACCGTCCGTGGGGTGCCCGTCGGCGTCACC
TCGGAGAGCGCCCGGGCAGCCTGGGTGGCGCTGATGAGCGAGCTCACGGGCGGCGTCGCTGGCTCGCCGCTGCGGCTCGC
CAACGGCAGCACGCCGTACTCGGGCTCGCAGGCTATGTACGGCCTGGCGCAGTGCACCAGGGACCTCAACGCCAGCGAGT
GCTCCAGCTGTGTCTCAAGCTACACGGACAGGCTGGGGGACCTGTTCCCCAACAACACCGGCGGCGCCATCAAGGGGTAC
AGCTGCTACCTGCGCTACCAGGTGGGCGTCCTCGACATCACCCTGCCGCCGGCGCCAACTCCCCCGGCGATATCCGTAGG
ACCTTCATCGTCTTCCAAGAGCGCCGATCATTCCAAGACCATCGGGATCCTGATCGGCGTGTTCGTCGGTTCCAGCTTGA
TAGCCCTGGTCTTCTTCATGCGACTCCCCCGGCGAAAGAGGGAAAAAAGTAAGCTCGTCGATGAAGAAGCAGCAAGAGAG
ATGGACGACGAGTTCGAGGAAGGGACCGGGCCAAAGCAGTTCCGCTACAGCGAGCTCGCCATGGCCACCGACTACTTCTC
GGACAAGCGCAAGCTCGGAGAAGGTGGGTTCGGGTCAGTGTACAGAGGCTACATTAAGGAGATGGACCTTCACGTCGCCA
TCAAGAGGGTGTCCAAGGGTTCGAAGCAGGGCAGGAAGGAGTACGCCTCGGAGGTCAGGATCATCAGCCTGCTGCGGCAC
CGTAACCTTGTGCAGCTCATCGGTTGGTGCCATGGCGGCGGCGAGCTCCTCCTCGTGTACGAGCTGATGCCCAACGGCAG
CCTCGACACGCACCTCTACAGCGCCAGGGACGGCGCCCTGCTGCCATGGCCGCTGCGGCACGAGATCGTGCTCGGCCTGG
GGTCGGCCCTGCTGTACCTTCATCAGGATTGGGAGCAGTGCGTTCTTCACAGGGACATCAAGCCGAGCAACGTGATGCTG
GACGCGTCCTTCCACGCCAAGCTCGGCGACTTCGGGCTCGCCAGGCTCGTCGGCCACGGCCGCCGCTCGCACACCACGGT
GATCGCCGGCACCTTGGGCTACATAGACCCCGACTGCATGATCACCGGCAGGGCCAGCACCGAGACTGACGTCTACAGCT
TCGGCGTCGTCCTCCTCGAGATCGCCTGCGGCCGGCGGCCTCTGGTGGCCGTT

Alignment

ORF - retro_sita_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.84 %
• Parental protein coverage: 85.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPPRLAVALATFALLCAAA---AGQDDKILRPWPPDCSTADNYTADSQYKKNLDQLLAALPAAAGDNGW
          MA........A..A.LC.AA....GQ.D.ILRPWPPDCSTADNYTADSQYKKNLDQLLAALPAAAGDNGW
Retrocopy MASRFFFLVVAVVARLCSAAMATGGQADDILRPWPPDCSTADNYTADSQYKKNLDQLLAALPAAAGDNGW

Parental  FYEGSVGTGAD-RVYGLIMCYADYNATACMDCLSRAPAGITTVCPGSRSVRAMYDACTLRYSAAPIPATA
          FYEGS.G.G.D..V.GLIMCYAD.NATAC.DCLSRAPAGI.TVCPGSR.VRAMYDAC.LRYSAAPIPATA
Retrocopy FYEGSAGAGTDDEVFGLIMCYADHNATACLDCLSRAPAGIATVCPGSRNVRAMYDACVLRYSAAPIPATA

Parental  DLAVLYIVYLTFP--EVAVTSEGVRAAWVPLMSELTGGAAASPLRLASGSTPYSSSQSSQEMYGLAQCSR
          DL..L..V..T.....V.VTSE..RAAWV.LMSELTGG.A.SPLRLA.GSTPYS.SQ....MYGLAQC.R
Retrocopy DLSYLHSVNGTVRGVPVGVTSESARAAWVALMSELTGGVAGSPLRLANGSTPYSGSQA---MYGLAQCTR

Parental  DLNASECSRCVSSYVGQLGKLFPNNSGGVIKGYSCYLRYQVAALDITLPPAPAPAT----PPPAGGPSSS
          DLNASECS.CVSSY...LG.LFPNN.GG.IKGYSCYLRYQV..LDITLPPAP.P......P.........
Retrocopy DLNASECSSCVSSYTDRLGDLFPNNTGGAIKGYSCYLRYQVGVLDITLPPAPTPPAISVGPSSSSKSADH

Parental  SKT-GIVVGVSVGSVSILILLGFSMWLLLRRRRRKEANLHEETRAMEDEFEKGSGPKRFRYGELAVATDN
          SKT.GI..GV.VGS...LI.L.F.M.L..R.R........E..R.M.DEFE.G.GPK.FRY.ELA.ATD.
Retrocopy SKTIGILIGVFVGSS--LIALVFFMRLPRRKREKSKLVDEEAAREMDDEFEEGTGPKQFRYSELAMATDY

Parental  FSDKYKLGEGGFGSVYRGFLKEMNLHVAIKRVSKGSNQGRKEYASEVRIISRLRHRNLVQLIGWCHGGGD
          FSDK.KLGEGGFGSVYRG..KEM.LHVAIKRVSKGS.QGRKEYASEVRIIS.LRHRNLVQLIGWCHGGG.
Retrocopy FSDKRKLGEGGFGSVYRGYIKEMDLHVAIKRVSKGSKQGRKEYASEVRIISLLRHRNLVQLIGWCHGGGE

Parental  LLLVYELMPNGSLDKYLHSADN--KLSWPLRHKIVLEIASAILYLHQEWEQCVLHRDIKPSNVMLDASFT
          LLLVYELMPNGSLD..L.SA.....L.WPLRH.IVL...SA.LYLHQ.WEQCVLHRDIKPSNVMLDASF.
Retrocopy LLLVYELMPNGSLDTHLYSARDGALLPWPLRHEIVLGLGSALLYLHQDWEQCVLHRDIKPSNVMLDASFH

Parental  AKLGDFGLARLVDHARGSHTTVAAGTLGYMDPERRARGRASARSDVYSFGVVLLEVACGRSPAVVL
          AKLGDFGLARLV.H.R.SHTTV.AGTLGY.DP.....GRAS...DVYSFGVVLLE.ACGR.P.V..
Retrocopy AKLGDFGLARLVGHGRRSHTTVIAGTLGYIDPDCMITGRASTETDVYSFGVVLLEIACGRRPLVAV

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_47 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	Si024562m.g	1 retrocopy	retro_sita_47 ,