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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtctaacagatcactcttctcagttgtttctttttaaataatatgtgcctcctcatgagttaggcacttattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG

Basic information

species Zea mays
transcript GRMZM2G165357_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
--cagtctaacagatcactcttctcagttgtttctttttaaata-atatgtgcctcctcatgagttaggcacttattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG
   |    |  | |    | ||   |   |||   |  ||  |  | | ||   |  |  |||| ||   |   ||| || |  || ||| ||||  ||| |||||||||| |||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
cttaagacactaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaa--attttg-accttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
cagtctaaca-gatcactcttctcagttgtttc-tttttaaataatatgtgcctcctcatgagttaggcacttattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG
 |   ||||| ||    |  | |||| ||     ||| |      | |  |     |  | | |||   |       ||||  ||  || |   ||    ||||||||| ||||   |  |  | || ||||| ||||||||||| ||||| ||||||||||| ||||||||||||||  |||||||||| |||
-aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaac-agATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
cagtctaaca-gatcactcttctcagttgtttc-tttttaaataatatgtgcctcctcatgagttaggcacttattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG
 |   | ||| ||    |  | |||  ||  |  |||||   |  | |  |   | |  | | |||   |       | ||  ||  || |   ||    ||||||||| ||||   |  |  | || ||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||  |||||||||| |||
-aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaatttaattaaaatgcatatacttttattttccctgaac-agATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG

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|148939205|gb|EC883670.2|EC883670
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32829264|gb|CD968942.1|CD968942
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211377009|gb|FL406724.1|FL406724
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|149065532|gb|EE286652.2|EE286652
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32787712|gb|CD936614.1|CD936614
EST:     AACCTGAAGAAGTGGATTGGCCACCCAAGNATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: AACCTGAAGAAGTGGATTGGCCACCCAAG-ATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211139565|gb|FL400395.1|FL400395
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211364308|gb|FL429333.1|FL429333
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211225658|gb|FL394160.1|FL394160
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211102135|gb|FL378499.1|FL378499
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32829447|gb|CD969125.1|CD969125
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211513418|gb|FL378838.1|FL378838
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32914071|gb|CF018883.1|CF018883
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211479897|gb|FL423797.1|FL423797
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTTGCT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTT-GCT
EST: gi|211264125|gb|FL402706.1|FL402706
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211355257|gb|FL372995.1|FL372995
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211057982|gb|FL426572.1|FL426572
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTT-CTTGTGGAAGTTGACCAAATCTATCACCTTGCT
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|71449953|gb|DR831003.1|DR831003
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211143536|gb|FL424879.1|FL424879
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211479918|gb|FL425086.1|FL425086
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32797525|gb|CD949761.1|CD949761
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211084498|gb|FL378036.1|FL378036
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32796729|gb|CD948965.1|CD948965
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32799379|gb|CD951615.1|CD951615
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211441206|gb|FL381374.1|FL381374
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32798044|gb|CD950280.1|CD950280
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211021925|gb|FL369377.1|FL369377
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211108221|gb|FL373168.1|FL373168
EST:     CAACCTGAAGAAGTGGATTGGCCAGCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|149070503|gb|EE158907.2|EE158907
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|15100352|gb|BI396143.1|BI396143
EST:     GAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: GAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211042612|gb|FL405104.1|FL405104
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211535769|gb|FL372741.1|FL372741
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT

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), 48 (downstream exon)
Score: 320

GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 850

GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1141

GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1744

GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcctcctcatgagttaggcacttattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG
                                    ttctttctatttgttt  CT-rich tract
                                taaattctttctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtctaacagatcactcttctcagttgtttctttttaaataatatgtgcctcctcatgagttaggcacttattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG

- - - - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - -tgcctcc