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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtgaaccttaggctagtacttactatgtttatggtcctactagcactcctgaagtcctattttgtttatggtcttggattcag

Basic information

species Zea mays
transcript GRMZM2G075488_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075488_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g06820.1 (Oryza sativa), 5'ss of exon 6
TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtgaacct-------taggctagta-cttactatgtttatggt-cctactagcactcctgaagtcctattttgtttatggtcttggattcag
|| || | |||| ||| |||||||||||||||||||||||| |||||||| ||||||||||| ||| ||||| |||  || |||       ||| || ||| | |   |   | ||  |   ||  |  | |  | ||||| | | || || ||||     |      
TTTGAGAGGTGGTTAGGTTTTGATCAAAATCCTCTTTATGCTCTCTTGCATGAGTCTATCTATTGTCAGgtacctttggagcctcatatgttagactggtagcatgagaacatcatattgtttagaacaattgttcaagtcttctcttattgatggatgcag------
















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|37377171|gb|CF625167.1|CF625167
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|37377054|gb|CF625098.1|CF625098
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|32928448|gb|CF033260.1|CF033260
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGTACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|32928122|gb|CF032934.1|CF032934
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|60358578|gb|DN225551.1|DN225551
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|32928342|gb|CF033154.1|CF033154
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|211492404|gb|FL232704.1|FL232704
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
EST: gi|67011936|gb|CO440685.1|CO440685
EST:     TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAG                         GGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT
genomic: TTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGT

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), 43 (downstream exon)
Score: 91

TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

TTCGAAATGTGGCTAGATTTTGATCAAAATCCTCTTTATGCCCTCTTGCACGAGTCTATCTACTGTGAGgtaacttgtg ... ttggattcagGGCTCTTCATCAAAATGGTCTGCTGAAAAGATTCATGGCGAATATGGGAGTTTGTTTGACCCTATTAAAGCTACAGAAGAAGGCCGAGCTGTGTACTTTA