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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttatatatttttagtttttccactaacctttgtcatcttttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA

Basic information

species Zea mays
transcript GRMZM2G174730_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 4
catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttata----tatttttagtttttccactaacctttgtcatcttttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
  |  |  ||  | || | |     |  ||      |   || |||   | ||| |    |  ||    ||| |  ||  | |||   | |  | | ||| |||||||| |||| || ||||| ||||| ||||| ||||||||||| ||||| |||||  | ||||| ||||| |||||||| ||||||||||| ||||||||
--tgcattgtctgctagcatttgtttctactgttgtagctaagatgccct-ttacaaagttgcttactatttatttacctaacttcacccttctct-tttgcagCTGGCATTGTCATTGAAGATAAAAATTGGCCACCCTTTTTCCCTCTCATTCACCATAATATTTCAAATGAGATACCTATTCATCTACAAAGAATGCAGTA

upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G37590.1 (Glycine max), 3'ss of exon 3
catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttatatatttttagtttttccactaacctttgtcatcttttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
              ||   | |    |   |  || |   ||        |    ||   ||||||||      | ||  ||      |||  ||| |||||||  |||| ||||| || ||||| ||||| || |||| |||| |||| || ||||||||| | |||||||||||||| ||||| |||   || |||||
-------------gtattttgagttcatctatacttacataacccaacaggaataatgcctttagtttggtggtttacactt-----ttttcttttgcagCTGGAATTGTTATAGAGGATAAAAATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTA

upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 3
catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttatatatttttagtttttccactaacctttgtcatcttttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
    |    |||  | |   ||| ||  |||   | |   || | | ||      ||   ||||||||      | ||  || |    || | ||| |||||||  |||| ||||| |||||||| ||||| || |||| |||| |||| || ||||||||| | |||||||||||||| ||||| |||   || |||||
----gtattttgagttcttcaacactttaca---taacccaacaggagta-----atgcctttagtttggtggtttacactttt---tttgtttttgcagCTGGAATTGTTATAGAGGAGAAAAATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTA

upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttatatatttttagtttttccactaacctttgtcatcttttatttt-cagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
              || | |   |   |  | | |    | | |     ||  || |  ||  |  |      || |   | |||||||||  |||   ||| ||  ||||||||||||||||||||||||| || ||||| || |||||||| || |||||||| ||||| ||||| |||||||| || || || || ||
-------------gtatctttgtcaatattatcttttgtagaaac---ctgacatttcgttccatgtgaaatgctcatgct-gtcatctttattttggtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA

upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G11180.2 (Arabidopsis thaliana), 3'ss of exon 4
----------------catagagggttggataccctaaccctaaacaccctg-aagaaatatgggttgttatatatttttagtttt---tccactaacct-ttgtcat----cttttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
                  |  |     |   |    ||        | |||   | | || |   |  |||   |||  |||| ||   ||||  |   |  | | ||    | ||| |||  ||| ||  |||| || || |  |||||||||||| |||| |||||||| |||||||| |||||| | |||||||| |   | | ||| |||||| | |||||
gtaaaacatctacctcttttcaacaccgaggatttgaatttagtgtaacctatgatatatgtctctgtttactgattcatagtcttgcttccataagtttgctcttatattacctttctttgtagCCGGAATTGTTATCGAGGCAAAAAACTGGCCTACCTTCTTCCCCCTTATCCACCATGACATTGCAAATGAAATTCTGGTTCGTCTCCAAAGGCTACAGTA

upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttatatatttttagtttttccactaacctt-tgtcatcttttatttt-cagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
       | |||  |    |     | |  |   ||||  ||| | |||||     | |||| |     || || | |    | ||||  ||| |||  |||||||  |||| ||||| |||||||| ||||| || ||||||||||| || || || |||||| | ||||||||||| ||||||| ||| | | |||||||
-------gtttgtctgttgtttatatcattag--tgaatcaat-taggttgagtagtgttttcatgcagtctacaatctaaatatcattctttctttggcagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA

upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ28229 (Selaginella moellendorffii), 3'ss of exon 4
catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttatatatttttagtttttccactaacctttgtcatcttttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
                                            |  | |||   | |||| |  | | | |  | |      | | |   | | | |||||||  |  |  |||| ||||| ||||||||||||||||||||  |||||| ||| ||||||      || || ||  | ||||| ||| |  | |||||
-------------------------------------------gtaagctgtc-cagatttattatgtcttcgatga------taaacaagtttatgcagCTGGAATCTTTCTAGAGGAGAAGAACTGGCCTCCCTTTTTCCCGATCATCCGCCATGACATTCGTCGCGACATTCCATTGCATCTTCAACGCCTACAGTA

upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ29726 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------------------catagagggttggataccctaaccctaaacaccctgaag----aaatatgggttgtt----atatatttttagtttttccactaacctttgtcatcttttatttt---cagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
                                    | ||||   ||  |||  |    |   |    |  |||    ||  |   | ||       ||   | |     |||    |  | |   | ||     | |||   |||||||  |  |  |||| ||||| ||||||||||||||||||||  |||||| ||| ||||||      || || ||  | ||||| ||| |         
gtagtcctctgttggaaatttttttcttccctccttaaagagaaatgcttactttgtttcaggagctgcgaaagctggaagcacaagctgcgcgaggtaagctgtccagatttattatgtcttggatgataaacaagTTTATGCAGCTGGAATCTTTCTAGAGGAGAAGAACTGGCCTCCCTTTTTCCCGATCATCCGCCATGACATTCGTCGCGACATTCCATTGCATCTTCAACG---------

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|149076952|gb|EE165608.2|EE165608
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211455821|gb|FL370764.1|FL370764
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|32828156|gb|CD967834.1|CD967834
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211251918|gb|FL397021.1|FL397021
EST:     GAATTGAAAAGGAWGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGHGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|32825089|gb|CD964811.1|CD964811
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|31353834|gb|CD438191.1|CD438191
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAATAAACTGGCCTCCCTTTTTCCCCCTCATC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAA-AAACTGGCCTCCCTTTTTCCCCCTCATC
EST: gi|211137749|gb|FL292364.1|FL292364
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211138691|gb|FL292374.1|FL292374
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211198979|gb|FL379473.1|FL379473
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTAGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211039428|gb|FL384648.1|FL384648
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211501973|gb|FL392126.1|FL392126
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|149069546|gb|EE157919.2|EE157919
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|76927277|gb|DV171213.1|DV171213
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211138685|gb|FL292368.1|FL292368
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211138688|gb|FL292371.1|FL292371
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|4152018|gb|AI372152.1|AI372152
EST:     GAATTGAAAAGGAAGGAAGATGCGGCATCCCGAG                         CTGGCGTTGTGATATAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211122269|gb|FL373644.1|FL373644
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|32825405|gb|CD965127.1|CD965127
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211138687|gb|FL292370.1|FL292370
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|76289053|gb|DV028621.1|DV028621
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|91872788|gb|EB402745.1|EB402745
EST:     GAATTGAAAAGGAAGGAAGAGGGGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAAATGGCCTCCCTTTTTTCCCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCC
EST: gi|71322127|gb|DR797759.1|DR797759
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211228158|gb|FL414420.1|FL414420
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGADAGAAGAGAAAAACTGGCCTCCCTTTTTSCCSCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|32808007|gb|CD960241.1|CD960241
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|149079646|gb|EE168643.2|EE168643
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|78081465|gb|DV509877.1|DV509877
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211130112|gb|FL389065.1|FL389065
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|78112246|gb|DV530640.1|DV530640
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|37417263|gb|CF646284.1|CF646284
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211035296|gb|FL425638.1|FL425638
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|211137579|gb|FL389525.1|FL389525
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
EST: gi|149104177|gb|EE289611.2|EE289611
EST:     GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAG                         CTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC
genomic: GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCC

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), 46 (downstream exon)
Score: 170

GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 141

GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 161

GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 208

GAATTGAAAAGGAAGGAAGAGGCGGCATCCCGAGgtacatttca ... ttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggttgttatatatttttagtttttccactaacctttgtcatcttttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA
                          cactaac  putative branch site (score: 208)
                                cctttgtcatctttta  CT-rich tract
      ttatatatttttagtt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catagagggttggataccctaaccctaaacaccctgaagaaatatgggttgttatatatttttagtttttccactaacctttgtcatcttttattttcagCTGGCGTTGTGATAGAAGAGAAAAACTGGCCTCCCTTTTTCCCCCTCATCCACCACGACATTTCCAATGAAATACCTATCCATCTACAAAGGATGCAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - -ccctgaa