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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggcttgtgacttcagagaatatttgcaccattattaatttgatgccagctaggatgtggcaatatgcctcactgattttatgattcgttctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG

Basic information

species Oryza sativa
transcript LOC_Os09g36450.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G852968_T03 (Zea mays), 3'ss of exon 7
----------------------------------------------------------------------------------aaggcttgtgacttcagagaata-tttgcaccattattaatttgatgccagctaggatgtggcaatatgcctcactgatttta------tgattcgttctgg--tacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG
                                                                                      ||||  ||    |     | |||||   |||| ||    |||  |   |   |  ||||   ||| | |  |||| | |      | ||| | ||||   | |||||||||| ||||||||||| ||||| ||||||||||||||||| ||||| || || || ||||||||||||||||| ||||||
gttggtttctcgtttcacataagctgtcaggataacgtgtttcgcgtgtttctttttccattaaatttgaaaatggaaagattgaacttggaaccgtggtttgcagtttgctaaattactatgaggataacgtgtttaacatggcttgatggccctgtgatgtgaccatcttcatttgctctgtgttgcagGTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCAAAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 8
aaggcttgtgacttcagagaatatttgcaccattattaatttgatgccagctaggatgtggcaatatgcctcactgattttatgattcgttctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG
                                                                                                                                       |||||||| ||||| || || || ||||||||||||||||| ||||||
---------------------------------------------------------------------------------------------------------------------------------------aAGAAAGAGGATATCGATGGTTTTCTTGTTGGTGGTGCCTCCTTGAAG

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G002807_T01 (Zea mays), 3'ss of exon 7
aaggcttgtgacttcagagaatatttgcaccattattaatttgatgccagctaggatgtggcaatatgcctcactgatt-ttatgattcgttc-tggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG
| |   ||| |  |   |    | |       |      ||| | |    ||        || || || |  |||||   |  |  || | |  || | |||||||||| ||||||||||| ||||| |||||||||||||||||||||||||| || || ||||||||||||||||||||||||
atgttctgttaaattttatttcagtgttgttgtggggtgtttaacgt--acttactgactgcgatgtgaccaactgaccatcctcctttgcttgtgttgcagGTTCTGTGAATGCAGCCAACTGTGCGGAGCTAGCAAAGAAAGAAGATATTGATGGTTTTCTTGTTGGTGGTGCCTCTTTGAAG

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 7
-------------aaggcttgtgacttcagag-aatatttgcaccattattaatttgatgccag-ctaggatgtggcaatatgcctcactgattttatgattcgt--tctggtacagGTTCTGTAAATGCAGCCAATT----GTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG------------------------
                 | |  |   ||||   ||  | |    | |  ||  |||      |   | | |  ||| || ||    |  ||      || || |   | || || |  | || | |    | |   ||     || |  | | ||   |  |   ||   |      || ||   || ||  |  ||| ||||                         
gttggtttctcgtttcacataagctgtcaggataacgtgtttcgcgtgtttctttttccattaaatttgaaaatggaaagattgaac-ttggaaccgtggtttgcagtttgcta-aattactatgaggataacgtgtttaacatggcttgatggccctgtgatgtgaccatcttcatttgctctgtgttgcagGTTCTGTGAATGCAGCCAACTGTGCAGAGCTAGCA

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 7
aaggcttgtgacttcagagaatatttgcaccattattaatttgatgccagctaggatgtggcaatatgcct---cactgattttatgattcgttctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG
|     |  || ||  |    |||||| |    || |  |||  | |    ||   ||  |||  || |      ||| |  | |   |    | |  | |||| ||||||||||||  |||  |||| ||||| |||||| ||||||||||||| || || |||||||||||||| || || |||
accatctcagaatt-ggttcttatttgaatg--taattttttttttcagaatacagtgcagcagcattctagaatactaacatcaaagtaatctgtctttcagGATCTGTAAATGCAAGCAACAGTGCTGAGCTTGCAAAGCAAGAAGATATTGATGGATTTCTTGTTGGTGGTGCTTCATTAAAG

upper sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 6
aaggcttgtgacttcagagaatatttgcaccattattaatttgatgccagctaggatgtggcaatatgcctcactgattttatgattcgttctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG
                         |||   |  |||| ||   || |    |  |||   |  ||||      ||||| |    |||    | |  |||||||||| |||| || |||  |||| ||||| || ||  ||||||| ||||| || || ||||||||||||||||| ||||||
------------------------gtgcgttag-attagttatctgtcg--caaaatgaaactttatg-----ttgattattgccttctcaattgc-cagGTTCTGTCAATGGAGGCAACAGTGCAGAGCTTGCCAAAGAAGAAGACATTGATGGATTTCTTGTTGGTGGTGCCTCCTTGAAG

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|8956697|gb|BE230372.1|BE230372
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATCTATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|86250549|gb|CI003667.1|CI003667
EST:     CATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCCATTGTGCCGAGCTAGCAAAGAAAGAAGATATGG
genomic: CATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|29645954|gb|CB650961.1|CB650961
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88847813|gb|CI005999.1|CI005999
EST:     TCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: TCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|86483625|gb|CI126258.1|CI126258
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|29678932|gb|CB675207.1|CB675207
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|29641345|gb|CB646352.1|CB646352
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|89170995|gb|CI040272.1|CI040272
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCGATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88959672|gb|CI002282.1|CI002282
EST:     AACCTACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|89168489|gb|CI038843.1|CI038843
EST:     ACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCCAAGAAAGAAGATATTG
genomic: ACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|33381301|gb|CF196644.1|CF196644
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAN                         NTTCTGTNNNTGCAGCCAATTGTGCCGAGCT
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCT
EST: gi|86527746|gb|CI167952.1|CI167952
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATAATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88844760|gb|CI021335.1|CI021335
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88993022|gb|CI035984.1|CI035984
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCGAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88988778|gb|CI039169.1|CI039169
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88841027|gb|CI000989.1|CI000989
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88904311|gb|CI002044.1|CI002044
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88966061|gb|CI012937.1|CI012937
EST:     TCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCCATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: TCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|58031138|gb|CX728681.1|CX728681
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|86522945|gb|CI163151.1|CI163151
EST:     ACCTGAGGTTGCTTCCGGCATTCGAATGATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: ACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|86524266|gb|CI164472.1|CI164472
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|29638544|gb|CB643553.1|CB643553
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|86250560|gb|CI003678.1|CI003678
EST:     CCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: CCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88215257|gb|CI215106.1|CI215106
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88216584|gb|CI214684.1|CI214684
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88221951|gb|CI221907.1|CI221907
EST:     GTTGCTTCCGGCATTCGAATTATATATGGAG                         TTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: GTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|87020131|gb|CI277863.1|CI277863
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88989919|gb|CI018796.1|CI018796
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|86902043|gb|CI300282.1|CI300282
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88221701|gb|CI221657.1|CI221657
EST:     CGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: CGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|66919184|gb|CX106032.1|CX106032
EST:     TGAGGTTGCTTCCGGCATTCGA-TTATCTATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: TGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|29686793|gb|CB683068.1|CB683068
EST:     AACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88224544|gb|CI222724.1|CI222724
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|29637218|gb|CB642227.1|CB642227
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|25802919|gb|CA758880.1|CA758880
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATCTATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|86528283|gb|CI168489.1|CI168489
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATCATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|86842390|gb|CI335282.1|CI335282
EST:     GGTTGCTTCCGGCATTCG-ATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATAGTT
genomic: GGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATA-TT
EST: gi|29628219|gb|CB633230.1|CB633230
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATCTATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|88849160|gb|CI087682.1|CI087682
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATNATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
EST: gi|86505521|gb|CI148154.1|CI148154
EST:     AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAG                         GTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG
genomic: AACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTG

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: 70 (upstream exon), 27 (downstream exon)
Score: 98

ACTCCTGAGCAAGCTCAGGAAGTTCATGCTGCTGTTCGTGATTGGTTGAAAACCAACGTGTCACCTGAGGTTGCTTCCGGCATTCGAATTATATATGGAGgtcggtttct ... tctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccagctaggatgtggcaatatgcctcactgattttatgattcgttctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG
                          cactgat  putative branch site (score: 98)
                                        ttcgttct  putative PPT
                               attttatgatt  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
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aaggcttgtgacttcagagaatatttgcaccattattaatttgatgccagctaggatgtggcaatatgcctcactgattttatgattcgttctggtacagGTTCTGTAAATGCAGCCAATTGTGCCGAGCTAGCAAAGAAAGAAGATATTGACGGCTTCCTTGTTGGTGGTGCCTCTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- -gcttgtg
- - - - - - - -agagaata
- - - - - - - - - - - - ttgcacc
- - - - - - - - - - - - - - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttatgat