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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgaaatcccagcaaatgaaacgtgcctcctggtttcaagcaccgtgcaaccagacttgttgagtcctcttgttgattttttggttaggttccttctgtctgctgtgctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGAGGAGGGGTCTAATTCTCTGTCGCGGTCTCCCCTGTCTACCTTCTTTGGT

Basic information

species Zea mays
transcript GRMZM5G809546_T01
intron # 1
splice site 3'
intron type U2

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|91055592|gb|EB166010.1|EB166010
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|37419824|gb|CF647597.1|CF647597
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|211153530|gb|FL067383.1|FL067383
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|71426547|gb|DR807597.1|DR807597
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|149098782|gb|EE184793.2|EE184793
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|211085341|gb|FL067379.1|FL067379
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACTCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|148963941|gb|EE015062.2|EE015062
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|50329513|gb|CO524639.1|CO524639
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|211153529|gb|FL067382.1|FL067382
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACTCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|149099086|gb|EE185106.2|EE185106
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|148960438|gb|EE153702.2|EE153702
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|211085340|gb|FL067378.1|FL067378
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACTCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|148936040|gb|EC880098.2|EC880098
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|149101791|gb|EE287390.2|EE287390
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|74244984|gb|DT652898.1|DT652898
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|211153533|gb|FL067386.1|FL067386
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|78106673|gb|DV525091.1|DV525091
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|71435836|gb|DR816886.1|DR816886
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|37421532|gb|CF648466.1|CF648466
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|71315713|gb|DR794488.1|DR794488
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|148980501|gb|EE027162.2|EE027162
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA
EST: gi|148951012|gb|EC896664.2|EC896664
EST:     GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAG                         GTGTACGCTGGAAACCGCCGGCCCTGGCTTCGACCCTCTGGGGCTCTACGA
genomic: GCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGA

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: 68

CGCGTGCCGTAGCGGCTGCGGCTCCCATCTATCCTCTCAGGCGCCGCATCGCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGAGGAGGGGTCTAATTCTCTGTCGCGGTCTCCCCTGTCTACCTTCTTTGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

CGCGTGCCGTAGCGGCTGCGGCTCCCATCTATCCTCTCAGGCGCCGCATCGCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGAGGAGGGGTCTAATTCTCTGTCGCGGTCTCCCCTGTCTACCTTCTTTGGT


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 35

CGCGTGCCGTAGCGGCTGCGGCTCCCATCTATCCTCTCAGGCGCCGCATCGCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGAGGAGGGGTCTAATTCTCTGTCGCGGTCTCCCCTGTCTACCTTCTTTGGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 59

CGCGTGCCGTAGCGGCTGCGGCTCCCATCTATCCTCTCAGGCGCCGCATCGCTATTACTACAACCAGAGGAAGGCGAGGCACACTGGACTGTTCCCCCAGgtaccgaaat ... gctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGAGGAGGGGTCTAATTCTCTGTCGCGGTCTCCCCTGTCTACCTTCTTTGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtcctcttgttgattttttggttaggttccttctgtctgctgtgctcgtgcagGTGTACGCTGGAAACCGCCGGCCCTGGCTTCTACCCTCTGGGGCTCTACGAGGAGGGGTCTAATTCTCTGTCGCGGTCTCCCCTGTCTACCTTCTTTGGT
         tgttgat  putative branch site (score: 59)
           ttgatttttt  TA-rich tract