RetrogeneDB ID: retro_sita_13

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 5:29967480..29969763(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si000409m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si016420m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_13
ATGGTCCAGATAGTAGACGACGTCGAGCGTGGCCCCGGGGCAGTGATCCCCGGAGCCGGGGAGGAGGACGACGACGAGGC
TTCACCAATCGAGGAGGTCCGCATGACCGTGCCGGCCACCGACGACCCGACGCTGCCGGTGTGGACATTCAGGATGTGGA
CTCTAGGGCTCCTCTCCTGCGTGCTCATGAGCTTCCTCAACCAGTTCTTCTCCTACCGCACCGAGCCCATCATCGTGACC
CAGGTCACCGTGCAGGTGGCCTCGCTCCCGCTAGGCCACTTCCTCGCGCGCGTGCTTCCCACCCGCAAGTTCAAGGCCCC
CGCGCTCCTCGGCGGCGGGGAGTGGAGCCTCAACCCGGGCCCCTTCAACATGAAGGAGCACGTGCTCATCTCCATCTTCG
CCAACGCCGGCTGCGCCTTCGGCAACGGCTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACCGCCGC
TCCATCTCCTTCTTCGCCGCGTGGCTGCTCATCACCACCACGCAGGTGCTCGGGTACGGCTGGGCGGGGCTCATGCGCAA
GTACGTCGTCGAGCCGGCGCACATGTGGTGGCCGGGCACCCTCGTGCAGGTGTCCCTGTTCCGGGCGCTGCACGAGAAAG
AGGACGACCAGCGGGTGGCCGAGGGCGGCGGCCCGCGCAGGACGTCGCGGGCCAAGTTCTTCCTGGTTGCGCTGGCCTGC
AGCTTCCTGTGGTACGCCGTGCCGGGCTACCTGTTCCCGACGCTGACCTCCGTGTCCTGGGTCTGCTGGATCTTCTCCAA
ATCGGTCACGGCGCAGCAGCTGGGGTCCGGCATGAGGGGCCTCGGCCTCGGCGCCTTCACACTCGACTGGACGGCCGTGT
CGTCGTTCCTCTTCAGCCCGCTGGTGTCGCCCTTCTTCGCCACCGCCAACATCCTGGCCGGGTTCGTGCTCTTCATGTAC
GTGATCGTGCCGGCGGCCTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTCTTCAT
GTTCAACGGGACGGGCTACGACATCAACGCGATCGTGAACGACCGGTTCGAGATCGACATGGACGCGTACCAGCAGCGCG
GGCGGATCAACATGAGCACCCTCTTCGCGCTAACGTACGGGCTCAGCTTCGCGGCGATCGCGGCGACCGTCACGCACGTC
GCGCTATTCCACAGCAAGGAGATCTACCGCCGCTTCCGCGCGTCGCAGAAGGACAAGCCCGACATCCACACGAGGCTGAT
GAAGAAGAACTACGAGGACGCGCCGGGCTGGTGGTTCTACTCGCTGCTCGTGCTGTCCGTGGCCGTCTCGCTCATCCTCT
GCACCGTCCTCAAGGAGGAGGTGCAGCTTCCCTGGTGGGGCCTGCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTG
CCAGTCAGCATCATCACGGCGACGACGAACCAGACGCCGGGGCTCAACGTCCTGTCAGAGTACGTCATCGGGCTGATACT
CCCCGGCAAGCCCATCGCCAATGTCTGCTTCAAGGTGTACGGCTACATGAGCATGTCGCAGGCCGTGTCATTCCTCCAGG
ACTTCAAACTCGGGCACTACATGAAGATACCCCCCAAGTCCATGTTCCTGGTCCAGTTCGTGGGGACGATCGTGGCCGGC
ACGGTGAACCTCGCGGTGGCGTACTGGCTGCTGGGCTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCCGCGGACAG
CCCGTGGACGTGCCCGAGCGACCGCGTCTTCTTCGACTCGTCCGTGATCTGGGGCCTCGTCGGCCCCCGCCGCATCTTCG
GGGCGCTGGGCAACTACGGCGCGCTCAACTGGTCCTTCCTCGTCGGCGCCGCGGGCCCCGCCATCGTGTACGGGCTCCAC
AAGGCGTTCCCGGGGCAGCGCTGGATACGGATGATCAACCTGCCGGTACTCATGGGCGCGACGGCCAGCATGCCGCCGGC
GACCGCCGTCAACTACAACTCATGGCTGCTGATCGGCATCGCCTTCAACTTCTTCGTGTTCCGGTACCGGAAGAAGTGGT
GGGAGCGATACAACTACATCCTCTCGGCGGCGCTGGACGCGGGCGTGGCGTTCATGGGGGTGCTGCTCTACTTCACGCTG
TCGATGGAGAACCGGAACATCAGCTGGTGGGGGACGGCCGGGGAGCACTGCCTGCTGGCGTCGTGCCCCACGGCGAGAGG
GGTGGATCTGGGCGCTGAGAGTGTCTGCCCCGTTGTCCTCTAA

Alignment

ORF - retro_sita_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.44 %
• Parental protein coverage: 70.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSRQISRSKFFLVALACSFAWYAVPGYLFPALTSISWVCWVFSKSVTAQQLGSGMKGLGLGAFTLDWSTV
          G.R..SR.KFFLVALACSF.WYAVPGYLFP.LTS.SWVCW.FSKSVTAQQLGSGM.GLGLGAFTLDW..V
Retrocopy GPRRTSRAKFFLVALACSFLWYAVPGYLFPTLTSVSWVCWIFSKSVTAQQLGSGMRGLGLGAFTLDWTAV

Parental  SSFLFSPLISPFFATVNIFFGYVFFVYLIMPIAYWGFNLYNAKTFPIFSSHLFMSNGTKYDIPSIVNSQF
          SSFLFSPL.SPFFAT.NI..G.V.F.Y.I.P.AYWG..LYNA..FPIFSSHLFM.NGT.YDI..IVN..F
Retrocopy SSFLFSPLVSPFFATANILAGFVLFMYVIVPAAYWGLDLYNARRFPIFSSHLFMFNGTGYDINAIVNDRF

Parental  ELDKDAYNQRGRVNLSIFFALSYGFSFATIAATITHVGLFYGKEIYRRFKASQKEKPDIHTKLMEK-YDD
          E.D.DAY.QRGR.N.S..FAL.YG.SFA.IAAT.THV.LF..KEIYRRF.ASQK.KPDIHT.LM.K.Y.D
Retrocopy EIDMDAYQQRGRINMSTLFALTYGLSFAAIAATVTHVALFHSKEIYRRFRASQKDKPDIHTRLMKKNYED

Parental  IPAWWFYSLMALSVVVSLLLCTVLKREVQLPWWGLIFACGMAFIFTLPISIITATTNQTPGLNVITEYAM
          .P.WWFYSL..LSV.VSL.LCTVLK.EVQLPWWGL.FAC.MAF.FTLP.SIITATTNQTPGLNV..EY..
Retrocopy APGWWFYSLLVLSVAVSLILCTVLKEEVQLPWWGLLFACAMAFVFTLPVSIITATTNQTPGLNVLSEYVI

Parental  GLIMPGYPIANVCFKVYGYMSMSQAVAFLSDFKLGHYMKIPPKSMFLVQFIGTIVAGTVNLGTAWWLLGS
          GLI.PG.PIANVCFKVYGYMSMSQAV.FL.DFKLGHYMKIPPKSMFLVQF.GTIVAGTVNL..A.WLLGS
Retrocopy GLILPGKPIANVCFKVYGYMSMSQAVSFLQDFKLGHYMKIPPKSMFLVQFVGTIVAGTVNLAVAYWLLGS

Parental  IKDICSDS-LPPESPWTCPSDRVFFDASVIWGLVGPRRIFGSAGNYGALNWFFLIGAAGPVIVYALHRMY
          I..IC.D..LP..SPWTCPSDRVFFD.SVIWGLVGPRRIFG..GNYGALNW.FL.GAAGP.IVY.LH...
Retrocopy IPNICQDALLPADSPWTCPSDRVFFDSSVIWGLVGPRRIFGALGNYGALNWSFLVGAAGPAIVYGLHKAF

Parental  PNQRWIPLINLPVLLGATASMPPATAVNYNSWLLIGTIFNFFVFRYQKKWWTRYNYILSAALDAGVAFMG
          P.QRWI..INLPVL.GATASMPPATAVNYNSWLLIG..FNFFVFRY.KKWW.RYNYILSAALDAGVAFMG
Retrocopy PGQRWIRMINLPVLMGATASMPPATAVNYNSWLLIGIAFNFFVFRYRKKWWERYNYILSAALDAGVAFMG

Parental  VVLYFSLTMENKTIDWWGTAGEHCPLASCPTAKGMDLGPDSVCPV
          V.LYF.L.MEN..I.WWGTAGEHC.LASCPTA.G.DLG..SVCPV
Retrocopy VLLYFTLSMENRNISWWGTAGEHCLLASCPTARGVDLGAESVCPV

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_13 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA005797	1 retrocopy	retro_oind_42,
Oryza nivara	ONIVA02G31600	1 retrocopy	retro_oniv_17,
Oryza sativa japonica	OS02G0695800	1 retrocopy	retro_osat_46,
Setaria italica	Si016420m.g	1 retrocopy	retro_sita_13 ,