RetrogeneDB ID: retro_sita_38

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 5:34194328..34196083(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si004646m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si000816m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_38
ATGGCCGGTGGAGGAGATGGCGGCGGCCTCGAGCTCGCCGCCGCCGCGGAGACGACGCTCGACGGGACGACGGACCACTC
CGGCAAGCCGGCGGTGCGGAGCAAGACGGGGACGTGGCGGGCGTGCCCCTTCATCCTCGGCAACGAGTGCTGCGAGCGCC
TCGCCTACTACGGCATGAGCTCCAACCTCGTCAACTACATGATCGACCGCCTCCACCAGGGGAACGCCGCCGCCGCCAAC
AACGTCAGCAACTGGTCGGGCACCTGCTACATGATGCCCCTCCTCGGCGCCTTCCTCGCCGACGCCTACCTCGGCAGGTA
CCGCACCATCGCCGCCTTCATGGGGCTCTACATCGTCGGCCTCACGCTGCTCACCATGAGCGCGGCCGTCCCGGGCCTTA
GGCCGCCCGACGCCGCCGGCGCGGCCCCGACCGCCGGGCAGAGCGCTGCATTCTTCGCTGCGCTCTACCTCATCGCCGTG
GGCACCGGCGGCATCAAGCCCTGCGTCTCCTCCTTCGGTGCCGACCAGTTCGACGACGCGGATCCGCGCGAGAGCCAGAG
CAAGAGCTCCTTCTTCAACTGGTTCTACACGTCCATCAACATCGGCGCTCTGGTCGCGTCGTCGGTGCTCGTCTGGATCC
AGATGAACGTGGGATGGGGCTGGGGCTTCGGCATCCCCGCCGTCGCCATGGCCGCGGCCGTCGCCAGCTTCCTGCTGGGG
AGCAGGCTGTACAGGCACCAGAGGCCGGGGGGCAGCCCGCTCACCCGGATGCTGCAGGTGGTGGTGGCCGCCTGGAGGAA
GAGGAAGTCGCCGGTGCCCGCTGACCCGTCCCTGCTCCACGAGGCGCCGGCGTCGGCGTCCGCCATCCAGGGCAGCAGGA
AGCTGGAGCACACGGAGCAGTTCCGGTGGCTCGACAGGGCCGCGGTGTTAACGGAGGAGGATGACACGATGAACAATGAG
AAGTCCAACCCGTGGCAGCTGTGCACGGTGACGCAGGTGGAGGAGCTCAAGAGCGTGGTGCGGCTGCTGCCGGTGTGGGC
GACGGGCATCGTGGTGTCGGCGGTGTACAGCCAGATGAGCACAATGTTCGTGCTGCAGGGCAACACGCTGGACCCGAGCG
TGGGCTCCAGCTTCAAGATCCCCTCGGCGTCGCTCTCCATCTTCGACACCCTGAGCGTCATCGCCTGGGCGCCCGTGTAC
GACCGCCTCATCGTCCCCGCCGCGCGGCGCTGGACGGGCCACCCGCGCGGCTTCACCCAGCTCCAGCGCATGGGCATCGG
CCTCGCCGTCTCCGTGCTGGCCATGGTCGCCGCGGGGGCCCTGGAGGTGCTCAGGCTCCACGTGGCGGCGTCGCACGGCA
TGCTCGACTCGACGGCCTACCTGCCCATCTCCATCTTATGGCAGGTGCCGCAGTACTTCATCATCGGCGCCTTCGAGGTG
TTCACCTTCATCGGCCAGATCGAGTTCTTCTACGACCAGGCGCCCGACGCCATGAGGAGCATGGGCACCGCGCTCTCGCT
CACCTCGTCGGCGCTCGGCAGCTACCTCAGCGCGCTGCTCGTGTCCGTCGTCACCGCCGTCACCACCAGGAACGGCGGCC
TCGGGTGGATCCCCGACAACCTCAACCGGGGCCACCTCGACTACTTCTTCTGGCTGCTCTCGCTGCTCAGCGTCATCAAC
TTCCTCGTCTACCTCTTGATTGCAAAGTGGTACAAGTACAAGCAGCCGTCCACTACCGCCGCAACGTCGACTTAG

Alignment

ORF - retro_sita_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.69 %
• Parental protein coverage: 96.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TQDGTVDIKGNPAVKKGTGNWRACPYILANECCERLAYYGMSTNLVNYMKTRLGQGNSIAANNVTNWSGT
          T.DGT.D..G.PAV...TG.WRACP.IL.NECCERLAYYGMS.NLVNYM..RL.QGN..AANNV.NWSGT
Retrocopy TLDGTTDHSGKPAVRSKTGTWRACPFILGNECCERLAYYGMSSNLVNYMIDRLHQGNAAAANNVSNWSGT

Parental  CYITPLIGAFLADAYMGRYWTIASFMIIYIIGLALLTMASSVKGLVPSCDISGTCHPTEPQTAVVFVALY
          CY..PL.GAFLADAY.GRY.TIA.FM..YI.GL.LLTM...V.GL.P..D..G...PT..Q.A..F.ALY
Retrocopy CYMMPLLGAFLADAYLGRYRTIAAFMGLYIVGLTLLTMSAAVPGLRPP-DAAGAA-PTAGQSAAFFAALY

Parental  LIALGTGGIKPCVSSFGADQFDENDAKEQKSKSSFFNWFYFSINIGALVASTVLVYVQTYVGWGWGFGIP
          LIA.GTGGIKPCVSSFGADQFD..D..E..SKSSFFNWFY.SINIGALVAS.VLV..Q..VGWGWGFGIP
Retrocopy LIAVGTGGIKPCVSSFGADQFDDADPRESQSKSSFFNWFYTSINIGALVASSVLVWIQMNVGWGWGFGIP

Parental  AVVMAIAVVSFFIGTPLYRHQRPGGSPITRIAQVLVASARKWSVAVPADKSLLHETPDGECGIKGSRKLE
          AV.MA.AV.SF..G..LYRHQRPGGSP.TR..QV.VA..RK....VPAD.SLLHE.P.....I.GSRKLE
Retrocopy AVAMAAAVASFLLGSRLYRHQRPGGSPLTRMLQVVVAAWRKRKSPVPADPSLLHEAPASASAIQGSRKLE

Parental  HTDQFGCLDKAAVETAADRTA----ASPWRLCTVTQVEELKSVVRLLPIWATGIVFATVYGQMGTMFVLQ
          HT.QF..LD.AAV.T..D.T.......PW.LCTVTQVEELKSVVRLLP.WATGIV...VY.QM.TMFVLQ
Retrocopy HTEQFRWLDRAAVLTEEDDTMNNEKSNPWQLCTVTQVEELKSVVRLLPVWATGIVVSAVYSQMSTMFVLQ

Parental  GNTLDQRMGPKFSVPSATLSMVDTISVIIWVPIYDRIIVPVVRSYTGRPRGFTQLQRMGIGLVISIFSMV
          GNTLD...G..F..PSA.LS..DT.SVI.W.P.YDR.IVP..R..TG.PRGFTQLQRMGIGL..S...MV
Retrocopy GNTLDPSVGSSFKIPSASLSIFDTLSVIAWAPVYDRLIVPAARRWTGHPRGFTQLQRMGIGLAVSVLAMV

Parental  AAGVLDIVRLRAVARHGLYGDKDVVPISIFWQIPQYFIIGCAEVFTFVGQLEFFYDQAPDAMRSLCSALS
          AAG.L...RL...A.HG........PISI.WQ.PQYFIIG..EVFTF.GQ.EFFYDQAPDAMRS...ALS
Retrocopy AAGALEVLRLHVAASHGMLDSTAYLPISILWQVPQYFIIGAFEVFTFIGQIEFFYDQAPDAMRSMGTALS

Parental  LTTVALGNYLSTVLVTIVTRITTRHGKLGWIPDNLNLGHLDYFFWLLAVLSLLNFLVYLVIASWYKYKK
          LT..ALG.YLS..LV..VT..TTR.G.LGWIPDNLN.GHLDYFFWLL..LS..NFLVYL.IA.WYKYK.
Retrocopy LTSSALGSYLSALLVSVVTAVTTRNGGLGWIPDNLNRGHLDYFFWLLSLLSVINFLVYLLIAKWYKYKQ

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_38 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC01G02400	1 retrocopy	retro_opun_3,
Sorghum bicolor	Sb03g006420	1 retrocopy	retro_sbic_24,
Setaria italica	Si000816m.g	1 retrocopy	retro_sita_38 ,