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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACAGGAGGTGGAACCCGAAGGTCTCGGACTTCGGCCTCGCCAAGCTCCTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtgagccgccgccgtgcttaaaattttgagcttcttcccttccggggtgaaatgaaatgtccgatcgatgtgagagttcctttcttttttgttggaag

Basic information

species Zea mays
transcript GRMZM2G147051_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147051_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g36050.1 (Oryza sativa), 5'ss of exon 4
TGGACAGGAGGTGGAACCCGAAGGTCTCGGACTTCGGCCTCGCCAAGCTCCTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtgagccgccgccgtgcttaaa-attttgagcttcttcccttccggggtgaaa----tgaaatgtccgatcgatgtgagagttcctttcttttttgttggaag
|||||| ||| |||||||| |||||||||||||| ||||||||||||||||| ||  | |||| |||||| || ||||| ||||| |||||||| |||||||  |  ||       |  || || ||   | | ||||    |    |    | ||  |    ||||   |  | ||  | ||    |   ||     ||||  |    
TGGACAAGAGATGGAACCCCAAGGTCTCGGACTTTGGCCTCGCCAAGCTCCTCGGTTCAGACAACAACTATGTTACCACGAGAGTCATGGGAACATTTGGgtaag-atggatg--tgaggttctcaattgtgtcgagcccggtgaaatgtaagatgtgagcactgaacactaaggtctctctggccatcgattctgcatttgcag----
















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|71762919|gb|DR960856.1|DR960856
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|93014131|gb|EB639651.1|EB639651
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|71308371|gb|DR790412.1|DR790412
EST:     CTGGGGGCGGACAGCAACTACGTCACCCCCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|30306478|gb|CD001151.1|CD001151
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|31909329|gb|CD650864.1|CD650864
EST:     ACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: ACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|30088116|gb|CB886321.1|CB886321
EST:     CACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|28987604|gb|CB351717.1|CB351717
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|28909856|gb|CB331133.1|CB331133
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|31909517|gb|CD650958.1|CD650958
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|31909295|gb|CD650847.1|CD650847
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|28987043|gb|CB351436.1|CB351436
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|71315686|gb|DR794464.1|DR794464
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|37396493|gb|CF635537.1|CF635537
EST:     CTGGGGGC-GACAGCAATTACGTCACCACCAGAGTGATGGG-ACGTTTGG                         CTACGTGGCCCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|29167724|gb|CB410984.1|CB410984
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|31909042|gb|CD650722.1|CD650722
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|29129799|gb|CB380503.1|CB380503
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|71439998|gb|DR821048.1|DR821048
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|31909331|gb|CD650865.1|CD650865
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: -TGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
EST: gi|29947207|gb|CB816535.1|CB816535
EST:     CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGG                         CTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA
genomic: CTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGA

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: 47 (upstream exon), 48 (downstream exon)
Score: 217

TGGACAGGAGGTGGAACCCGAAGGTCTCGGACTTCGGCCTCGCCAAGCTCCTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

TGGACAGGAGGTGGAACCCGAAGGTCTCGGACTTCGGCCTCGCCAAGCTCCTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 28

TGGACAGGAGGTGGAACCCGAAGGTCTCGGACTTCGGCCTCGCCAAGCTCCTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 62

TGGACAGGAGGTGGAACCCGAAGGTCTCGGACTTCGGCCTCGCCAAGCTCCTGGGGGCGGACAGCAACTACGTCACCACCAGAGTGATGGGAACGTTTGGgtgggtgtga ... ttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC