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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG

Basic information

species Zea mays
transcript GRMZM2G155242_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 3'ss of exon 6
-------------gtgggaacc--tagtatctctcttctattaagatgaag-tgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcat----gcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
              |   | ||  | |      | |   ||| | | |  | | || ||  || || |    ||  |  |  | ||  |    | |||   |||  |    | ||||||||||||| || ||||||||||||||||| || || |||||||||||||| || || |||||||||||| | ||||||||||||||||||||||| |
gtaccaaccatatatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataagaactttggcttttgttttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAACCTTTCCGCACCTCAAACATTCCGATCCAAGGAGATCTCCAAGAGCAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------gtgggaacctagtatctctcttctat-taagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattt--tcat--gcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
                                                               ||      | |||      || |   |      |  | | | | |   |||||  |  || |   | | | ||  |  | |||  ||  | ||   ||||| || || || || || ||||||||  |||||||||| ||||| ||||| || || || || ||||| ||| | |||||||| ||||||||||||||||
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaat-gagttgattttttcaagtgttctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G31450.4 (Glycine max), 3'ss of exon 3
------gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatg-acgttattgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
       ||    | ||   | |   |   || ||  |||||    | || || | | | || ||  ||  ||   |    | | |      |      ||||| || || || ||||| ||||||||  |||| ||||| ||||||||||| || || ||||||||||| ||| | || ||||| |||||||||||||| |
gattttttgtatgcttaaactttaattaaaataaaattgaagaacgtgttggggagaagtacattgatg--atgttttaattgtctgggtgatgagtgacagCCAACATCTATAGTGAGTTACAACCATCTGGGCAACAATGATGGCATGAATCTCTCAGCCCCTCAAACCTTCCGCTCTAAGGAAATCTCCAAGAGCAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------------------gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaa-taactcttctatattttcattttcatg-----cagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
                                                                                          | | |  ||   |  |   ||  | ||| || || |  | | ||||| ||  | |     | || |   | || || ||| || |  | |||     ||||| || || || ||||| |||||||| ||||||||||| ||||||||||| || || ||||||||||| ||| | || ||||| || ||||||||||| |
gtacaacttttgttgttttgcttactaatactattgctatatcacgtgtgctactacttttattggttaataataaggacagagtatcatttgtatgcttaaactttaattaaaataaaataaaataatgtgttggctaaaaatggagaagtaaattgatgtttta-attgtcttggtgatgagtgacagCCAACATCTATAGTGAGTTACAACCATTTGGGAAACAATGATGGCATGAATCTCTCAGCCCCTCAAACCTTCCGCTCGAAGGAAATTTCCAAGAGCAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
    | || || |          |||    || || | || ||||      | ||||||    |  || |    |  ||||   | |   |  |||| || || || || || ||||||||  | || |||||||| ||||||||| |||| || |||||||||||| |||| |||||||| || |||||||| |
----gtacttaatcctaaataagtatcctaattaaat-ttattttatatggtaacgttacaaaacgaaattaattgcatttatctatatgtatagCCGACGTCGATTGTCAGTTACAACCATCTTGGGAACAACGACGGCATGAACTTGTCAGCACCTCAAACATTCCGGTCAAAGGAGATATCGAAGAGCAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgtta-ttgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
            || | | | |||  |||| |  | |||     ||     | |||| || | ||| ||  || || | |   || | | ||||  ||    |  |||| || ||||| ||||||||||| |||||||||||||||||||| ||||| || || || || || || ||||| || |||||||||||||| ||||| |
gtttgtttaacttgcgtatcaagttactctttcttgttactgaaaa-----tatttgtcacaagactttggtttcattga---ttgtgtgtttttgtt----tatagCCTACTTCAATTGTGAGCTACAATCACTTGGGAAACAACGATGGAATGAATCTCTCAGCTCCACAGACTTTCAGATCTAAGGAGATCTCCAAAAGCAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatg-cagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
                         || | ||  ||| || |      ||     |  |||| |   | |     || | ||      ||| |   |   | ||  | ||  |  || ||||| || || || |||||||| |||||  |||||||||||||||||||||| |||||||| |||||||| ||| | ||||||||||||||||||||||| |
gtatatcatttttagcatttcctctgttgaaatttagaattt------taaagtaaataagtatgcatgtataggattatgtatgaataatgatattgaaagatgatgatggtggtgacagCCAACATCCATTGTGAGCTATAACCATCTGGGAAACAACGATGGCATGAATCTGTCTGCTCCTCAAACCTTCCGCTCCAAGGAGATCTCCAAGAGCAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 3'ss of exon 6
gtgggaacctagtatctctctt---ctattaagatgaagtgtttttttggcaaatg------acg--ttattgcaataactc---ttctatattttc--attttcatgca--gCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
|||    |  || |||||  ||     | |   |  |   | || | |   ||  |      | |  || |  | ||   ||   ||||  || |    ||| |  ||||  |||||||||||| ||||||||||| || |||||||||||||||||||||||| |||| || ||||| || ||  | ||||||||||||||||| ||||| |
gtgattcctaagcatctcgtttggttcactggaagtatccggttctctttaaatcgttttctatggtttgtcacgatgtatcctgttctgaatctctgaattattgtgcacagCCCACCTCAATTGTGAGCTACAATCATTTGGGAAACAACGATGGCATGAACTTGTCAGCACCTCAGACCTTTCGTTCCAAGGAGATCTCCAAAAGCAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------------gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
                                                                                                  ||    | ||    | | |  | |   ||| || | || ||  |      ||||     ||||| | |  |  | || | ||  | | ||  ||||| || ||||| || ||||||||||| ||||| ||||||||||| |||||| |||| ||||||||||||||| | ||||||||||||||||||||||| |
gtgagccaagtgcaatgtgtagaggaataaatgtaataaagccttctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgct------atgaaagctttgcactgaacccacaat-tgttggtgtgca--cagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAACTTGTCCGCCCCTCAAACATTCCGTTCCAAGGAGATCTCCAAGAGCAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ27629 (Selaginella moellendorffii), 3'ss of exon 6
gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
                               | || | |  ||||      |    || || | |       |||| ||     || || | ||||| ||||| || || |||||||| ||  | || ||||| ||||| ||||| || ||||| |||||||||||||| |||||||| |||||||||||||| |
------------------------------gtaaaatctcgtttttc----tcgtatttttccgac------tctaaatccgtcttgtcttccagCCAACCTCCATTGTCAGCTACAATCATCTTGGTAACAATGATGGAATGAATCTATCTGCGCCTCAAACATTCAGATCCAAGGAAATCTCCAAGAGCAATG

upper sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 6
gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
                               | || | |  ||||      |    || || | |       |||| ||     || || | ||||| ||||| || || |||||||| ||  | || ||||| ||||| ||||| || ||||| || ||||||||||| |||||||| |||||||||||||| |
------------------------------gtaaaatctcgtttttc----tcgtatttttccgac------tctaaatccgtcttgtcttccagCCAACCTCCATTGTCAGCTACAATCATCTTGGTAACAATGATGGAATGAATCTATCTGCGCCGCAAACATTCAGATCCAAGGAAATCTCCAAGAGCAATG

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|32838843|gb|CD978524.1|CD978524
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|31352226|gb|CD436583.1|CD436583
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32925788|gb|CF030600.1|CF030600
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32926333|gb|CF031145.1|CF031145
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|211029036|gb|FL245282.1|FL245282
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32859828|gb|CD999509.1|CD999509
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|211029043|gb|FL245289.1|FL245289
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32843100|gb|CD982781.1|CD982781
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32924916|gb|CF029728.1|CF029728
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32925548|gb|CF030360.1|CF030360
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACTGATGGCATGAA
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAAC-GATGGCATGAA
EST: gi|31353688|gb|CD438045.1|CD438045
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32863171|gb|CF002853.1|CF002853
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32925926|gb|CF030738.1|CF030738
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|211029042|gb|FL245288.1|FL245288
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32843595|gb|CD983276.1|CD983276
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32924885|gb|CF029697.1|CF029697
EST:     CCAAGATGAAGTCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|31352116|gb|CD436473.1|CD436473
EST:     CCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|4776520|gb|AI665523.1|AI665523
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|6536588|gb|AW224901.1|AW224901
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
EST: gi|32864017|gb|CF003699.1|CF003699
EST:     CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAG                         CCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC
genomic: CCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAAC

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: 549

TATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 43

TATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 18

TATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 118

TATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtgggaacct ... tttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG
                      caataac  putative branch site (score: 118)
                            ctcttctatattttca  CT-rich tract
                               ttctatattttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggaacctagtatctctcttctattaagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
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