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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaagcttttttttctctgctatgtgcttgtgatggtgggattgcaaaatctatttttctgttaaatgctcaccagctatttcttgaacttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCGAAAATGCTGTTTTCACCATTCCTCCTGATTTGGCCTATGGTGAATCTGG

Basic information

species Oryza sativa
transcript LOC_Os08g41390.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 2
-----------cacaagcttttttttctctgctatgtgcttgtgatggtgggattgcaaaatctatttttctgttaaatgctcaccagctatttcttgaacttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCGAAAATGCTGTTTTCACCATTCCTCCTGATTTGGCCTATGGTGAATCTGG
           |       |  |  | | |      ||| | |  || ||  ||||| || |  |    |      ||||||||  | ||||||  | ||    |  ||||||||||||||||| |||||||||| ||| |||||||||||||||||||| ||||||||| |||| ||||||||||| ||  |||| ||||| | ||||||
gtaaattctagcttggagatcatcctgtttctctcttgcctctt-tgttgacattgccaagttgaaaaat------aatgctcattaactattttgtcaa----tgcccagGTCAAGTGATAAAGGGTTGGGATCAAGGAATCAAGACCATGAAGAAAGGAGAAAATGCTATTTTTACCATTCCTCCAGAGCTGGCTTATGGAGCATCTGG

upper sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G11240.1 (Glycine max), 3'ss of exon 1
cacaagcttttttttctctgctatgtgcttgtgatggtgggattgcaaaatctatttttctgttaaatgctcaccagctatttcttg-aacttgt---atccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCGAAAATGCTGTTTTCACCATTCCTCCTGATTTGGCCTATGGTGAATCTGG
    |  || || || |     |  ||    | |   |    |    ||   |   |   ||   ||   |      | || | |||  |||||    || |||| |||||||| || || ||||||  ||||||||| |||||||||||||| || |||||  ||||||| || || || || ||||| ||||| || || ||
----aatttattgttatactggacatgaaaattaaacttaagtgattaatgatgaatggatgaataactatagtattcaatgttttgtgacttgactaatgcagGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG

upper sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G28260.1 (Glycine max), 3'ss of exon 1
cacaagcttttttttctctgctatgtgcttgtgatggtgggattgcaaaatctatttttctgttaaatgctcaccagctatttcttg-aacttgt---atccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCGAAAATGCTGTTTTCACCATTCCTCCTGATTTGGCCTATGGTGAATCTGG
    |  || |  || |     |  ||    | |   |    |    ||   |   |   ||   ||   |      | || | |||  |||||    || |||| ||||||||||| || ||||||  ||||||||| |||||||||||||| || |||||  ||||||| || || || || ||||| ||||| || |||||
----aatttatccttatactggacatgaaaattaaacttaagtgattaataatgaatgaatgaataactatagtattcaatgttttgtgacttgattaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCGGAATTGGCTTATGGAGAGTCTGG

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|8858040|gb|AU095358.1|AU095358
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|88316943|gb|CI625580.1|CI625580
EST:     GATTCAAGCCGTGACCCGTGGGACAACCTT-AAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAG
genomic: GATTCAAGCCGTGACC-GTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAG
EST: gi|58655964|gb|CK044644.1|CK044644
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|8858050|gb|AU095368.1|AU095368
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGGATCTAGGTATCAAGACCATGNAAGAAAGG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGG-ATCTAGGTATCAAGACCATG-AAGAAAGG
EST: gi|58690253|gb|CK078940.1|CK078940
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|88394593|gb|CI605934.1|CI605934
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTAT
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTAT
EST: gi|58690739|gb|CK079426.1|CK079426
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|88409713|gb|CI569003.1|CI569003
EST:     GATTCAAGCCGTGACCGCTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCA-GTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGATGAAAGG
genomic: GATTCAAGCCGTGACCG-TGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGG
EST: gi|88361507|gb|CI605288.1|CI605288
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|1631494|gb|C19223.1|C19223
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58665256|gb|CK053942.1|CK053942
EST:     TGATTCAAGCCGTGACCGTGGGACACCCCTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58675334|gb|CK064021.1|CK064021
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGACAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58694438|gb|CK083125.1|CK083125
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|88394916|gb|CI607643.1|CI607643
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATC
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATC
EST: gi|58687081|gb|CK075768.1|CK075768
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|88324708|gb|CI626913.1|CI626913
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTT
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTT
EST: gi|58675080|gb|CK063767.1|CK063767
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|88387790|gb|CI587878.1|CI587878
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGG
EST: gi|218486102|gb|FG952697.1|FG952697
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|88421837|gb|CI611716.1|CI611716
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACC
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACC
EST: gi|218492631|gb|FG962246.1|FG962246
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58667007|gb|CK055693.1|CK055693
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTA
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTA
EST: gi|4880950|gb|AU065249.1|AU065249
EST:     AGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: AGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|29624443|gb|CB629454.1|CB629454
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|88343363|gb|CI621731.1|CI621731
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGT
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGT
EST: gi|58608921|gb|CK036954.1|CK036954
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58668442|gb|CK057128.1|CK057128
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGAACATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58670205|gb|CK058891.1|CK058891
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58683729|gb|CK072416.1|CK072416
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58682636|gb|CK071323.1|CK071323
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|88358456|gb|CI608356.1|CI608356
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|29675035|gb|CB671310.1|CB671310
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|33380928|gb|CF196271.1|CF196271
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|29666721|gb|CB662996.1|CB662996
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|29626371|gb|CB631382.1|CB631382
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58608216|gb|CK036249.1|CK036249
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCCAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58610628|gb|CK038340.1|CK038340
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|58665497|gb|CK054183.1|CK054183
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
EST: gi|29628610|gb|CB633621.1|CB633621
EST:     TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAG                         GTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG
genomic: TGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCG

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 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 67 (downstream exon)
Score: 113

TACACTACACTGGCACACTGCTTGATGGAAAGAAGTTTGATTCAAGCCGTGACCGTGGGACACCCTTCAAGTTTAAGTTGGGACAAGgtacaattcc ... ttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCGAAAATGCTGTTTTCACCATTCCTCCTGATTTGGCCTATGGTGAATCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaatctatttttctgttaaatgctcaccagctatttcttgaacttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCGAAAATGCTGTTTTCACCATTCCTCCTGATTTGGCCTATGGTGAATCTGG
                      tgctcac  putative branch site (score: 113)
       tatttttctgttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacaagcttttttttctctgctatgtgcttgtgatggtgggattgcaaaatctatttttctgttaaatgctcaccagctatttcttgaacttgtatccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCGAAAATGCTGTTTTCACCATTCCTCCTGATTTGGCCTATGGTGAATCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
cacaagc
- - - - - - - -ctctgct
- - - - - - - - - - - - gtgcttg
- - - - - - - - - - - - - - - - gatggtg
- - - - - - - - - - - - - - - - - - - - gattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcttg