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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTATTTTCGATAATTACAGTCATGTCATTCTTCCTGTTGGCCCCGGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcctgctgcttattttttcatgataccttataagactagcttgggcagaattctatatttatgaatattgtttcttgtgcag

Basic information

species Zea mays
transcript GRMZM2G103047_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103047_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 5'ss of exon 6
TCTATTTTCGATAATTACAGTCATGTCATTCTTCCTGTTGGCCCCGGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcctgctgcttattttttcatga-taccttataagactagcttgggcagaattctatatttatgaatattgtttcttgtgcag
 || || || || |||||||| |||||||||||||| |||||||| |||||||| || ||||| ||||| ||||| | |||  ||||| |||||||||||||||| | | || |  ||| || |  |  | |  ||  | | |     || ||   |||| |  | |     || || |||||| || ||
CCTCTTCTCAATCATTACAGTGATGTCATTCTTCCTCTTGGCCCCAGTAACCTTGCTAACAGAGGGTGTCAAAGTCACTCCGACAGTTCTGCAGTCTGCTgtgagcaccttgatatttaattatagacaaattgctccttacatattgtttggtgcaatttttgact-----attttctttcttatgtag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211421922|gb|FL203902.1|FL203902
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|37380935|gb|CF627314.1|CF627314
EST:     GTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTCCTGCATGCTGC
genomic: GTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|83279029|gb|DV943037.1|DV943037
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|149070711|gb|EE159127.2|EE159127
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|71427133|gb|DR808183.1|DR808183
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|211046748|gb|FL449688.1|FL449688
EST:     TTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: TTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|78121641|gb|DV540025.1|DV540025
EST:     AAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: AAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|149007368|gb|EE040218.2|EE040218
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTTTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|148999233|gb|EE036153.2|EE036153
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|76916103|gb|DV166240.1|DV166240
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|111193309|gb|EE291445.1|EE291445
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|60357212|gb|DN224185.1|DN224185
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|50334493|gb|CO529619.1|CO529619
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|211345606|gb|FL479616.1|FL479616
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|91054475|gb|EB164893.1|EB164893
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|60349346|gb|DN216319.1|DN216319
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|37383666|gb|CF628857.1|CF628857
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|91054476|gb|EB164894.1|EB164894
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|83278332|gb|DV942340.1|DV942340
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|76018096|gb|DT945266.1|DT945266
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|78110414|gb|DV528826.1|DV528826
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|60343683|gb|DN210656.1|DN210656
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|101401959|gb|EB822602.1|EB822602
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|74235577|gb|DT643491.1|DT643491
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|4753301|gb|AI657206.1|AI657206
EST:     CTTACTTACAGAAGGNGGTAAAGTTAGTCCAACANTTTTGCAAG-CTGCT                         GGTTTGAACTTGAAACAGATATACACA
genomic: CTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCA-GTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACA
EST: gi|211114341|gb|FL479353.1|FL479353
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|78110415|gb|DV528827.1|DV528827
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|71444330|gb|DR825380.1|DR825380
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGGTGCATGCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
EST: gi|37383669|gb|CF628859.1|CF628859
EST:     CTTAC-TATCAGAAGGTGTTAAAGTTAGTCCAGCAGTTTAGCAGTCTGCT                         GGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC
genomic: CTTACTTA-CAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

TCTATTTTCGATAATTACAGTCATGTCATTCTTCCTGTTGGCCCCGGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGCTTCCATGCATACCAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 176

TCTATTTTCGATAATTACAGTCATGTCATTCTTCCTGTTGGCCCCGGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGCTTCCATGCATACCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

TCTATTTTCGATAATTACAGTCATGTCATTCTTCCTGTTGGCCCCGGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGCTTCCATGCATACCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

TCTATTTTCGATAATTACAGTCATGTCATTCTTCCTGTTGGCCCCGGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTTTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGATATACACAAGGTCATTGATTGCTGCATGCTGCTTCCATGCATACCAACAG