Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatagtgccatatccattttctatatcttattttcgtagattttcctttgattctatggtattgtcataggtcatattcatgaagttttgtttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA

Basic information

species Zea mays
transcript GRMZM2G151580_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 2
----gatagtgccatatccattttctatatcttattttcgtagattttcctttg-attctatggtattgtcataggtcatattcatgaagttttgtttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA
     ||  ||   ||||||| |  |  |     || |    ||| |   | |  | | | || |||| |  | |  |||| | |||||| || | |  ||||||||||||||||| ||||||||| ||||||| || ||||||||||| |||||||| || |||||||||||||| ||  | |||||||||||||||||||| |
tctgaatgctggtgtatccatctctttaaaaagcttct----gatctgaatatatactatgtgttattat-gttgaccatactgatgaagattggatctccacagGATGATAAAAATATTGCTCATCTGACTCACGTTAGTGAGATGGAGAAGAAGTGTGAATCTTTGGCCAGAATCACCACTATTTTGAAAGATGTAATTCAAA

upper sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 3
--------------------------------------------------gatagtgccatatccattttct-atatcttattttcgtagattttcctttgattctatggtattgt-cataggtcatattcat--gaagttttgtttg--ccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA
                                                  | | |      ||  ||||||| | ||        |  |    ||| ||||||  |||  ||   |  ||  ||| || ||||    || |||||         ||||||| |||||  |||| |||||||||||||||||||| ||||||||||||   ||| | ||||| || || ||| | ||  | |||||||| |||||||
gttagccttttagccattccagttgtatctggaccatctgacgtttactagttggctaagaattaattttctgacataagtaaaaccaatgccttcttttgatgttattttaacttatatctgtc-tactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA

upper sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G38820.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------gatagtgccatatccattttctatatcttattttcgtagatt--ttcctttgattctatggta--ttgtcataggtcatattcatgaagttttgtttg--ccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA
                                                  | | ||     ||  |||||||  |  | | |       |||  ||| ||||||  |||  ||  ||||    |   |      |  || |||||         ||||||| |||||  |||| |||||||||||||||||||| ||||||||||||   ||| | ||||| || || ||| | ||  | |||||||| |||||||
gttagccttttagccattccagttgtatctggaccatctgatgtttcctagttggttaagaattaattttctg-acataagtaaaaccaattccttcttttgatgttattttaacttgtatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA

upper sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 2
-gatagtgccatatccattttctatatcttattttcgtagattttcc--tttgattctatggtattgtcataggtcatattcatgaagttttgtttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA
  |   |    | |   | |  | || |||   |  ||  ||||     ||| || ||  |   ||   |   | ||| ||  |  | ||  | |||    |||| ||||| ||  | || ||| | || ||||| ||||| |||||||||||||| ||| |||| || || || ||||| || ||||||||||| ||||| |
caaggataattttttggtctctttta-cttgaatctgtttatttgaaaattttatactgggcacttcctaactgacatgtttgttgaattg-gattgtt-tagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAGTGTGAGACTTTAGCAAGGATTACTGCTATATTGAAAGATGTTATTCAAA

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|211093052|gb|FL420423.1|FL420423
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|8383242|gb|BE056185.1|BE056185
EST:     GTGGATCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: GTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211100223|gb|FL405650.1|FL405650
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAATAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211451594|gb|FL373081.1|FL373081
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211111976|gb|FL386053.1|FL386053
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|76934754|gb|DV174014.1|DV174014
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211482108|gb|FL397167.1|FL397167
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|28910110|gb|CB331266.1|CB331266
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211209474|gb|FL385668.1|FL385668
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|74245692|gb|DT653606.1|DT653606
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|113701683|gb|EE679187.1|EE679187
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|149079676|gb|EE168672.2|EE168672
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|148965294|gb|EE016099.2|EE016099
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211079651|gb|FL402142.1|FL402142
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|101394443|gb|EB819156.1|EB819156
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|31350966|gb|CD435323.1|CD435323
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211223287|gb|FL370924.1|FL370924
EST:     TCATGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211469271|gb|FL411607.1|FL411607
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211526759|gb|FL372689.1|FL372689
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATG-AAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|31352195|gb|CD436552.1|CD436552
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|149059488|gb|EE156973.2|EE156973
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|78110457|gb|DV528867.1|DV528867
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211060466|gb|FL406471.1|FL406471
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211134623|gb|FL369505.1|FL369505
EST:     TCGTGCACAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211469566|gb|FL427738.1|FL427738
EST:     TCGTGCAGAGGAACATTGTCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|22545500|gb|BU097859.1|BU097859
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211313156|gb|FL384840.1|FL384840
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211511087|gb|FL380251.1|FL380251
EST:     CGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: CGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGG-AAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|86467153|gb|DY233523.1|DY233523
EST:     TCGTGCAGAGGAACTTTGCCAACTTGCAAGTGGAGCTACGGGGAAAAAAG                         GATGATAAAAACATTGCTCATTTGACTCGTGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|101391367|gb|EB817618.1|EB817618
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211093054|gb|FL420425.1|FL420425
EST:     CGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: CGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGG-AAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211032703|gb|FL419052.1|FL419052
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211105662|gb|FL427074.1|FL427074
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|211023129|gb|FL428619.1|FL428619
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
EST: gi|22473167|gb|BU037647.1|BU037647
EST:     TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAG                         GATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG
genomic: TCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAG

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: 102

TAGCTCCGACAAAAGCGATGATTTGGTGAAGGTTTTGAGGGAACTGACTGTCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 67

TAGCTCCGACAAAAGCGATGATTTGGTGAAGGTTTTGAGGGAACTGACTGTCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 57

TAGCTCCGACAAAAGCGATGATTTGGTGAAGGTTTTGAGGGAACTGACTGTCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

TAGCTCCGACAAAAGCGATGATTTGGTGAAGGTTTTGAGGGAACTGACTGTCGTGCAGAGGAACATTGCCAACTTGCAAGTGGAGCTACAGGGAAGAAAGgtgatgtttt ... tttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgattctatggtattgtcataggtcatattcatgaagttttgtttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA
 ctttgat  putative branch site (score: 74)
                                        ttttgttt  putative PPT
                            atattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatagtgccatatccattttctatatcttattttcgtagattttcctttgattctatggtattgtcataggtcatattcatgaagttttgtttgccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - -tgccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attcatg