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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCTGTTGAATGCAATCGCTAACCAACTGCGCTATCCAAATAGCCATACACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgagatgggtttaatgttgtttgcacgtccccttgtatggttctctaataatgtccgtggtatgcag

Basic information

species Zea mays
transcript GRMZM2G065130_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065130_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g01240.1 (Oryza sativa), 5'ss of exon 40
CCTTCTGTTGAATGCAATCGCTAACCAACTGCGCTATCCAAATAGCCATACACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgagatgggtttaatgttgt-ttgcacgtccccttgtatggttctctaataatgtccgtggtatgcag----------------------
|||| | ||||||||||| |||||||| ||||| || || |||| ||||||||||| || || ||||||||  ||| |||| ||||| || |||||||||||||| | |||| | |      | |  ||     | | ||||| |       |  |   ||      |||  |                       
CCTTGTTTTGAATGCAATAGCTAACCAGCTGCGTTACCCTAATATCCATACACACTGCTTCTACTTCATCATCCTGCATCTGTTTTCAGAAGCTACCCAGgtatttc-agatagctcattcctcgagttattgattctcttgtttatactgttgtttgcgttaagaatatataaacatcgcaatgggaatatgcag
















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|32933969|gb|CF038781.1|CF038781
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|28983531|gb|BQ539575.2|BQ539575
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|33100958|gb|CF060918.1|CF060918
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|7145572|gb|AW507053.1|AW507053
EST:     TATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: TATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|32935273|gb|CF040085.1|CF040085
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|12046716|gb|BF728855.1|BF728855
EST:     TCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: TCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|74243503|gb|DT651417.1|DT651417
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|28983873|gb|BQ538838.2|BQ538838
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|211523269|gb|FL465590.1|FL465590
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|211523268|gb|FL465589.1|FL465589
EST:     CACASTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTWCCCAGGAGCAAATCACAAGGGKTYTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|60400854|gb|DN233661.1|DN233661
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|113701130|gb|EE678634.1|EE678634
EST:     TATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: TATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|211448996|gb|FL452553.1|FL452553
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|166602194|gb|EG102796.1|EG102796
EST:     TTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: TTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|44901063|gb|CK827608.1|CK827608
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|45847106|gb|CN071049.1|CN071049
EST:     TATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCCCAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: TATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|37386121|gb|CF630236.1|CF630236
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|32847419|gb|CD987100.1|CD987100
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|15427149|gb|BI542971.1|BI542971
EST:     CCCACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|241994794|gb|GR421147.1|GR421147
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|31358677|gb|CD443034.1|CD443034
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|16925324|gb|BM078392.1|BM078392
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|67021500|gb|CO450249.1|CO450249
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
EST: gi|32847417|gb|CD987098.1|CD987098
EST:     CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAG                         GAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG
genomic: CACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTG

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: 159

CCTTCTGTTGAATGCAATCGCTAACCAACTGCGCTATCCAAATAGCCATACACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTGAACCGCCCCCATCCTTGGGGGTTACTTATTACTTTCATTGAATTGATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

CCTTCTGTTGAATGCAATCGCTAACCAACTGCGCTATCCAAATAGCCATACACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTGAACCGCCCCCATCCTTGGGGGTTACTTATTACTTTCATTGAATTGATAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

CCTTCTGTTGAATGCAATCGCTAACCAACTGCGCTATCCAAATAGCCATACACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTGAACCGCCCCCATCCTTGGGGGTTACTTATTACTTTCATTGAATTGATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

CCTTCTGTTGAATGCAATCGCTAACCAACTGCGCTATCCAAATAGCCATACACACTACTACTCCTTCATCACTCTGTATCTATTTTCCGAGGCTACCCAGgtattgcgag ... tggtatgcagGAAATTACCCAGGAGCAAATCACAAGGGTTCTTCTGGAGCGTCTCATAGTGAACCGCCCCCATCCTTGGGGGTTACTTATTACTTTCATTGAATTGATAA