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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtgcgctgtacggctagctagtttttccttcagagagattgatcgagatgtgacgatgccgctgccttggttgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC

Basic information

species Zea mays
transcript GRMZM5G836250_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 2
gcaagtgcgctgtacggctagctagtttttccttcagagagat-tgatcgagat-gtgacgatg----ccgctgccttggttgct-cgac-agGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC
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gcaagtgtacctggcaa-taactgtcatctttctcagtttcttgtctctgagattgagatagtgaggactgaggacttgcttggtgtgaccagGGAGAGGAGCAGAAGAAGCTGGACGTGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC
















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|148938587|gb|EC882914.2|EC882914
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|78106830|gb|DV525248.1|DV525248
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|50332539|gb|CO527665.1|CO527665
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|50331045|gb|CO526171.1|CO526171
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|37420508|gb|CF647945.1|CF647945
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAG
EST: gi|78105897|gb|DV524315.1|DV524315
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
EST: gi|78113532|gb|DV531923.1|DV531923
EST:     AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAG                         GGAGAGGAGCAGAAGAACCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG
genomic: AGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAG

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: 26 (upstream exon), 24 (downstream exon)
Score: 1

GCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 93

GCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 9

GCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

GCTCTCCCACATCGTCCTCGGCTGCAAGTTCGTCGCCTCCGCCGTCAACAAGGCCGGGCTCGCCCAGCTCATCGGGCTCGCCGGCGAGACCAACGTGCAGgcaagtgcgc ... tgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcagagagattgatcgagatgtgacgatgccgctgccttggttgctcgacagGGAGAGGAGCAGAAGAAGCTGGACGTCCTGTCCAACGAGGTGTTCGTCAAGGCCCTCGTCAGCAGCGGTCGCACC
          gattgat  putative branch site (score: 76)