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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttaatttgaattgtctagggtctgaaatagttcaagcccctaatgactagagttgattattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG

Basic information

species Oryza sativa
transcript LOC_Os04g51630.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 5
--attttaatttgaattgtctagggtctgaaa-tagttcaagc--ccctaatgactagagttgattattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
  |   |   |  ||| |   || ||||| |  |||||   ||  |  |  |   |         |  | ||   ||| ||| | |  |   |||| |   |||||||||| || |||||||||||| | || |||||||||||||||||||| ||||| || |||||||| || ||||||||  | |||||| |||||||||||
aaaacattgctacaatag--gagagtctggaggtagttactgcatctttgcttggtgactccagcttctcatgaccttgctaaactgatatatcttgt---ttagGTACCCGAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTACGGAAAACTGAACAAGCAGAGGATCCCTCTGTCTAACAACCAAGTCATCGAG

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
-attttaatttgaattgtctagggtctgaaatagttcaagcccctaatgactagagttgat----tattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
 |    |   | ||  |  ||  ||||| | ||||||  ||  || |          | ||    |   |||   |||||||   | |  | |||| |   ||||||||||||| ||||| |||||| | || |||||||||||||||||||||||||| || |||||||| || ||||||||  | |||||| |||||||||||
gaaaaaagcataaa--gcatactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgt---ttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094051_T03 (Zea mays), 3'ss of exon 5
attttaatttgaattgtctagggtctgaaatagttcaagcccctaatgactagagttgat----tattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
     ||  | ||      || | ||| | ||||||  ||  || |          | ||    |  ||||   ||||||| | | |  | |||| |   ||||||||||||| |||||||||||| | || ||||||||||||||||||||||||||||| |||||||| || ||||||||  | |||||| |||||||||||
-aaaaaacataaagcagacagtgcctggagtagttcctgcatcttagcttggtgactcatctgcttctgatgaccttactaaagtggcaaatcttgt---ttagGTACCCAAACTTGAAGAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAAGCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 5
attttaatttgaattgtctagggtctgaaatagttcaa-gcccctaatgactagagttgattattgatcttcttactagattagtgattcttatg------ttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
                      ||  |  | ||||||| | |  | ||    | |  || ||  | | || |      | ||  | ||  ||          || |||||||| ||||||||||||||    |||||||||||||||||||||||||||||  | |||||||| |||||  |  | |   |||||    |  | || 
----------------------gtaagtgaaagttcaacgacattgattgtcata--tggttcattacctgcaccacgggttcttaatatttgcaaatccacttcagGTACCCTAATTTGAAGAGTGTAAAAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAA

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G23750.2 (Glycine max), 3'ss of exon 5
attttaatttgaattgtctagggtctgaaatagttcaagcccctaatgactagagttgattattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
          | ||  |       |||  ||| ||  |     | |||| || || |  ||||  | || || |  ||| |  ||   ||| |||||||| ||||||||| | ||||||||  | ||| | || |||||||| || ||||||||||| |||||||| || |   |||| ||  |||||    |||| |||
----------gtatgtttacttccctgccatactt--atttaattatgattataggtttttat--aactgctaatgagacttctg---cttttgttttagATACCCAAATCTTAAGAGTGTGAGAGAACTTATTTACAAGAGAGGGTATGGAAAGCTAAACAAGCAGAGGACTGCTCTAACTGACAACTCCATCATTGAG

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 5
attttaatttgaattgtctagggtctgaaatagttcaagccc-ctaatgactagagttgattattgatcttcttactag-attagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
                      ||  |  | |||||||   |  | ||    |  ||| ||||         |   |   | || |      |    || |||||||| ||||||||||||||  | |||||||||||||||||||||||||||||  | |||||||| |||||  || | ||| |||||    | || || 
----------------------gtaagtgaaagttcaactacattgattctcatggttcattacctgcaccatggttcttaatatttgcaaatccacttcagGTACCCTAATTTGAAGAGTGTTAGAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCTTTGACAGACAACTCTATTATTGAA

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0054g00030.t01 (Vitis vinifera), 3'ss of exon 4
attttaatttgaattgtctagggtctgaaatagttcaagcccct---aatgactagagttgattattgatcttct-tactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
         | | |     |   | ||   |  || ||  ||     || | ||| | |||  || |  || | | || |  |||  |  |||  || |||||||||||| |||||||||||||| || |||||||| ||||||||||| || |||||| | |||||||| ||||   |  | ||  |||||    |  | || 
--------gtaagtatctcactctttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttgtaatgtatttatatttcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAATTGATTTACAAGAGGGGGTACGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0054g00210.t01 (Vitis vinifera), 3'ss of exon 5
------attttaatttgaattgtctagggtctgaaatagttcaagcccctaatgactagagttgattattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
      || ||| | |   |||| |      | ||||  |  ||     |    ||| | ||  |||||| |  ||  || |  |||  |  | |  || |||||||||||| |||||||||||||| || ||| |||| ||||||||||||||||||||| | |||||||| ||||   |  | ||  |||||    |  | || 
gtaagtatcttactct--tttgttttt--cttaaaatcctataaaaagttctgaacttgtgt--attattca--tttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
attttaatttgaattgtctagggtctgaaatagttcaagcccctaatga-----ctagagttgattattgatc-ttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
         | | |    ||   | |    |   | |||  ||||   |     ||  | |||  ||||  || ||  || |  |||  |  | |  || |||||||||||| |||||||||||||| || ||| |||| ||||||||||||||||||||| | |||||||| ||||   |  | ||  |||||    |  | || 
------gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 5
attttaatttgaattgtctagggtctgaaatagttcaagcccctaatgactagagttgattattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
              ||| |   | |||  |   |   | ||   |  ||  | |  |    ||  |   | ||| |    || |||   ||  |||| ||||| || ||||| ||||||||| | ||| |||| ||||||||||| |||||||| || |||||||| ||||   |||| ||  | |||  | |||| || 
-----------gtatgtgttctgactgccaacttcataaccttcagggatcatatctccacatgcaatctgttattcatatactgaagatt--gtttcagGTATCCCAATTTAAAGAGTGTCAGGGAACTGATTTACAAGAGGGGTTATGGAAAACTTAACAAGCAGAGAACTGCTCTGACTGATAACTCAATCATTGAA

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 4
attttaatttgaattgtctagggtctgaaatagttcaagccccta----atgactagagttgattattgatc-ttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
         | | |     |   | |    |   | ||   ||||    | | ||| | |||  || |  || ||  || |  |||  |  | |  || |||||||||||| ||||||||||||||  | |||||||| ||||||||||| ||  ||||| | |||||||  ||||   |  | ||  |||||    |  | || 
--------gtaagtatctcacccttttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGTGAGAATTGATTTACAAGAGGGGGTACAGAAAGTTGAACAAGCTGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 4
attttaatttgaattgtctagggtctgaaatagttcaagccccta----atgactagagttgattattgatc-ttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
         | | |     |   | |    |   | ||   ||||    | | ||| | |||  ||||  || ||  || |  |||  |  | |  || |||||||||||| |||||||||||||| || |||||||| ||||||||||| ||||||||| | |||||||| ||||   |  | ||  |||||    |  | || 
--------gtaagtatctcactcttttgtttttcttaaaatcctataaaaagtctaaacttgtatattattcatttctaatgtatttatattgcaaatattttagGTACCCCAATTTGAAGAGTGTGCGAGAATTGATTTACAAGAGGGGGTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA

upper sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 3
---------------------attttaatttgaattgtctagggtctgaaatagt-tcaagcccctaatgactagagttgattattgatcttcttactagattagtgattc-ttatgttt-tagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
                     | |    |||| |   | |    |   ||   || |   |||      |||| |   ||  | ||||  |  | || || |  |   |   || || ||  |||||||| |||||||||||||| |||||||||||||| ||| | ||  | || ||| |   ||||  | |  || | |||||  |||| |   | ||||||
gtaggcagcgaatggcgtaaaactgagttttggagaatttcattttgaaagaggtgttttgccttccccgacttgttctggat-ttgaattgatcacgagttcggctttcaattgtgcttgcagGTACCCTAATTTGAAGAGTGTTCGTGAATTGATCTATAAGCGTGGGCACGGTAAGGTTGTCAAGTCACGTGTCGCCCTTACTGACAATACCATTATCGAG

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|2797323|gb|AA750617.1|AA750617
EST:     AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
EST: gi|86527124|gb|CI167330.1|CI167330
EST:     AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
EST: gi|29618048|gb|CB623060.1|CB623060
EST:     AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
EST: gi|86899550|gb|CI327449.1|CI327449
EST:     AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
EST: gi|29618050|gb|CB623062.1|CB623062
EST:     AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
EST: gi|88276870|gb|CI396033.1|CI396033
EST:     ATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: ATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
EST: gi|29641909|gb|CB646916.1|CB646916
EST:     AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
EST: gi|27577886|gb|CB000581.1|CB000581
EST:     AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
EST: gi|27554300|gb|CA998200.1|CA998200
EST:     AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: AAAGCCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
EST: gi|15847027|gb|BI795303.1|BI795303
EST:     CCACCATTAACATGCTGCGCA-GGTTGA-CCATATGTTGCATATGG                         GTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG
genomic: CCACCATTAACATGCTGCGCAGGGTTGAGCCATATGTTGCATATGGgtaagctacc ... tatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgactagagttgattattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
                       ttcttac  putative branch site (score: 2)
                                         ttcttat  putative PPT
                                        attcttatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttaatttgaattgtctagggtctgaaatagttcaagcccctaatgactagagttgattattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA