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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgcctccttcccctccccgtccccctccctgatttttgagtgatctagcctgatccgggtctaatgctgcccgcccttcctgaattttcctctgccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG

Basic information

species Zea mays
transcript GRMZM2G540403_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 3'ss of exon 2
---gtccgcctccttcccctccccg--tccccctccctgatttttg----------agtgatctagcctgatccgggtctaatgctgcc-cgcccttcctgaa-ttttcctctgccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG
    | | |||||| | |||||||   | ||| || |   ||  ||          ||  ||||| || || ||| |||||||||| || ||  ||   ||   || |  ||| | ||||||||| |||||| | || ||||||||||| ||||| ||||| || |||||||| || || ||||| || |||||||||
gtgcttctcctcctcctcctccccaaattcccttctcgtgttcatgcgagctgacgagcaatctaacccgacccgagtctaatgctaccgcgatctctttgttcttctgttcttctgtggtagGTGGTGAAGCATGAAGGGTGGGAGCGGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAG
















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|149109204|gb|EE190074.2|EE190074
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|78112113|gb|DV530509.1|DV530509
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|149071944|gb|EE160331.2|EE160331
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|78120502|gb|DV538886.1|DV538886
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|211496381|gb|FL046952.1|FL046952
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACG
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACG
EST: gi|88756340|gb|DY540481.1|DY540481
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|148952677|gb|EC898511.2|EC898511
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|91877627|gb|EB407584.1|EB407584
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|211175056|gb|FL087597.1|FL087597
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|8367157|gb|BE050102.1|BE050102
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|71766550|gb|DR964487.1|DR964487
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|148964459|gb|EC905815.2|EC905815
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|76936044|gb|DV174582.1|DV174582
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|148957275|gb|EC903307.2|EC903307
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|149027549|gb|EE046558.2|EE046558
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|211175053|gb|FL087594.1|FL087594
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|149013466|gb|EE042980.2|EE042980
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|71448089|gb|DR829139.1|DR829139
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|78121537|gb|DV539921.1|DV539921
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|91051844|gb|EB162262.1|EB162262
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
EST: gi|211175055|gb|FL087596.1|FL087596
EST:     ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTG                         GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT
genomic: ACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCT

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: 106

GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 147

GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 150

GTGAACGCGCGGCAACAGACGGAGCGCGACCCCTCCAAGCCGGCGTTCAAGGACGGCGCCGCTCGCCAGTTGTATCTGgtccgcctcc ... gccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgatccgggtctaatgctgcccgcccttcctgaattttcctctgccgtggtagGTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG
          gtctaat  putative branch site (score: 150)
                                    ttttcctctgccgt  putative PPT
                                tgaatttt  TA-rich tract