RetrogeneDB ID: retro_sita_19

Retrocopy location

• Organism: Foxtail millet (Setaria italica)
• Coordinates: 3:1524289..1525336(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Si024494m.g
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Si030277m.g
• Aliases: None
• Description: None

Sequence

>retro_sita_19
ATGTCTTCGGGAATTCAAGACAGTGAGGTTGACATTGTGATCGCAGCACTCCAGCCCAACCTGAACACCTTCTTTGAAGC
ATGGCGGCCATTTTTCTCTCGTTTCCACATCATTGTTGTCAAAGATCCAGACATGAAAGAGGATCTTCAAATCCCCACTG
GCTTTGATCTCAAGGTTTACACCAAGTCAGATATTGATGGAATGCTTGGCGCCACGTCCATCAACTTCTCCGGTCACTCA
TGCCGTTACTTTGGGTATCTTGTCTCACGCAAGAAGTATGTGATTTCAATTGATGACAATTGCCTCCCAGCAAAGGACAC
GGCTGGGTCGACTGTTGATGCTGTTGCGCAGCACATGGTCAATTTGAAGACACCCGCCACGCCTTTCTTTTTCAACACAC
TCTATGATCCATACAGGAAAGGTGCTGATTTTGTCCGTGGTTACCCATTCAGCCTGCGCGAAGGGGTTGACTGCATGCTC
TCATGTGGTTTGTGGCTGCATAACGCGGACTACGACCCAATGACTCATGTTGTGAAGAGAAATCAGCGGAACACAACCTA
TGTGGATGCTGTGATGACAGTTCCGCTTGGCGCCATGATGCCTGTGAGTGGGATAAACGTTGCATTCAACCGTGAGGTAT
TGGGGCCTGCTATGTTCCCAGCCCTCCGGCTACGCAACGAAGGGAAGCACAGATGGGATACCCTTGAAGACGTATGGAAT
GGTTTGTGTGCTAAAGTGGTATGCGACAGCTTGGGGTATGGTATGAAGACTGGACTGCCTTATGTGATGAGAAGTGATGC
GGAAGCAGGTAAAGCTCTGGAGAGTTTGAAAGAATGGGAAGGAGTGAAAGTCATGGATGATGTTCTTCCATTCTTCCAAT
CACTCAAACTATCAAGGACTGCAGTTACTGTTGAAGATTGTGTTAAGGAGCTAGCAAGCATCGTCCGGGAGAAACTAGGA
CCAAAGAATGCAATCTTCACCAAAGCAGCCGATGCCATGGTGGAATGGAACAACCTCTGGAAGTCTCATGGAGCTCGGAA
TGCTTAG

Alignment

ORF - retro_sita_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.6 %
• Parental protein coverage: 90.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELDIVIPTIR-NLD-FLEMWRPFFQPYHLIIVQDGDPNKTIRVPEGFDYDLYNRNDITRMLGPKATCISF
          E.DIVI.....NL..F.E.WRPFF...H.I.V.D.D.......P.GFD...Y...DI..MLG..AT.I.F
Retrocopy EVDIVIAALQPNLNTFFEAWRPFFSRFHIIVVKDPDMKEDLQIPTGFDLKVYTKSDIDGMLG--ATSINF

Parental  KDSACRCFGYMVSKKKYIYTIDDDCFVAKDPSGKDINALEQHIKNLLSPSTPFFFNTLYDPYRDGADFVR
          ....CR.FGY.VS.KKY...IDD.C..AKD..G....A..QH..NL..P.TPFFFNTLYDPYR.GADFVR
Retrocopy SGHSCRYFGYLVSRKKYVISIDDNCLPAKDTAGSTVDAVAQHMVNLKTPATPFFFNTLYDPYRKGADFVR

Parental  GYPFSLREGVPTAVSHGLWLNIPDYDAPTQLVKPLERNTRYVDAILTIPKGTLFPMCGMNLAFDRELIGP
          GYPFSLREGV....S.GLWL...DYD..T..VK...RNT.YVDA..T.P.G...P..G.N.AF.RE..GP
Retrocopy GYPFSLREGVDCMLSCGLWLHNADYDPMTHVVKRNQRNTTYVDAVMTVPLGAMMPVSGINVAFNREVLGP

Parental  AMYFGLMGDGQPIGRYD---DMWAGWCTKVITDHLGLGVKTGLPYIWHSKA-SNPFVNLKKEYNGIFWQE
          AM...L........R.D...D.W.G.C.KV..D.LG.G.KTGLPY...S.A.........KE..G.....
Retrocopy AMFPALRLRNEGKHRWDTLEDVWNGLCAKVVCDSLGYGMKTGLPYVMRSDAEAGKALESLKEWEGVKVMD

Parental  ELIPFFQSVSLPKEATTVQKCYLELAKQVRAKLGKVDGYFNKLADAMVTWIEAW
          ...PFFQS..L...A.TV..C..ELA..VR.KLG.....F.K.ADAMV.W...W
Retrocopy DVLPFFQSLKLSRTAVTVEDCVKELASIVREKLGPKNAIFTKAADAMVEWNNLW

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_19 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_2g461970	1 retrocopy	retro_mtru_4,
Prunus persica	PRUPE_ppa007588mg	1 retrocopy	retro_pper_48,
Setaria italica	Si030277m.g	1 retrocopy	retro_sita_19 ,