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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaagttggaatttgattatgtcgtaaaatatatgcaccctacatgttttagcttcatattgacttatattttcatatgtgctccttcaactgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA

Basic information

species Oryza sativa
transcript LOC_Os01g08700.8
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G107101_T01 (Zea mays), 3'ss of exon 11
caaagttggaatttgattatgtcgtaaaatatatgcacccta-catgtt-ttagcttcatattgactta--tattttcatatgtgctccttcaactgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
    |||  ||       | || | ||| ||  | |   |||   | || ||  |||| | |||  ||    |||||  | | ||  |||| |||| |   ||| ||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||  || | ||||||||||| || ||||||||||||||||||||||
---tgttataacaacccaaagtaggaaattagcttccttctaatttattgttgacttctttttgcattgatcatttttctgtctgaacctt-aactaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATTGCTTCTTTGTTGTGTGCTCATGGCCCTGATGTTGAGTGGAGAATATGTA

upper sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 10
caaagttggaatttgattatgtcgtaaaatatatgcaccct-acatgtt-ttagcttcatattgactta--tattttcatatgtgctccttcaactgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
  | |||  ||       | || | ||| ||  | | || | |  | ||  |  ||||   |||  ||    |||||| | | ||| |||   ||| |   ||| ||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||  || | ||||||||||| || ||||||||||||||||||||||
--atgttataacaaacgaaagttggaaattagcttccccttgatttattgctgacttctgtttgcattgatcattttcctgtctgcacct--gactaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATTGCTTCTTTGTTGTGTGCTCATGGGCCTGATGTTGAGTGGAGAATATGTA

upper sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G36600.2 (Glycine max), 3'ss of exon 10
----------------------caaagttggaatttgattatgtcgtaa--aatatatgcaccc-tacatgttttagcttcatattgacttatattttcatatgtgctccttcaactgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
                       | | ||  | |||  ||||||  |    ||| | | ||  |   |||||     |||    |  ||||    | | | |  |      |  |        || | |||||||||||| |||||||| ||||||| || ||||| ||||||||||| || ||||| ||||| |||||||| || ||||| |||||||| || |
gttgtgttcacctttatcagttaacatttttattttctttatgttattcttaatttgtacagtcactcatgtagattctttccgtacacttgagatctaaaacatttgttgttgatc------agATAGAAGTTCCTGCAGCTGAAGCCTCTATTGAAGCTACTGCCCAAGGCATTGCATCAATGCTTTGTGCCCATGGTCCAGAGGTTGAATGGAGAATTTGCA

upper sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 4
---------------caaagttggaatttgattatgtcgtaaaatatatgcaccctacatgttttagcttcatattgacttatat-tttcatatgtgctccttcaactgcacaa-agCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
                  ||||   ||||  || | | | |  ||   |      ||||     |  | |    |      |||   || | || |    | |    ||   |  || | |||||||||||| |||||||| | ||||| || ||||| ||||||||||| || ||||| ||||| |||||||| || ||||| |||||||| || |
gttgtgtgcaactttatcagttaacatttttttttcttg-attattcttattttttacagtcactcacgtagattctttccatacacttgaaatctaaaacctttgttgttgatcagATAGAAGTTCCTGCAGCTGAAGCCTCAATTGAAGCTACTGCCCAAGGCATTGCATCAATGCTTTGTGCCCATGGTCCAGAGGTTGAATGGAGAATTTGCA

upper sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G07240.2 (Glycine max), 3'ss of exon 10
caaagttggaatttgattatgtcgtaaaatatatg-caccctacatgttttagct--tcatattgacttatattttcatatgtgct-----ccttcaac-------tgcacaa-agCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
           || | |||     |  ||  ||   ||   | |   ||||   |  | || | ||  ||  | || ||   ||||      ||  ||        ||   |  || | |||| | || || | |||||||||||||| || || || ||||||||||| ||  |||| || ||||||||||| || || ||||||||||| ||||
----------gttcggttactctttgcaagttacctcatttttctcattttgtatggtaatgtagagctaattctttatgcatgctgaagatctataatatatatttgtctatcagATTGAAGCTGCTTCAGCCGAAGCCACTATTGAAGCTACGGCCCAAGGCATTGCCTCAGTGCTTTGCGCTCATGGTCCAGAGGTAGAGTGGAGAATTTGTA

upper sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
-caaagttggaatttgattatgtcgtaaaatatatgcaccctacatgttttagcttcatattgacttatattttcatatgtgctccttcaactgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
 ||  |||    |||   | | ||    | |  ||      ||   | ||    |||   | ||    ||| || | |    ||| ||  |   || | || | |||||||||||| | ||||| || ||||| |||||||| ||||| ||||| || ||||| |||||||||||||| || |||||||||||||| || |
gcatggttcctctttatatttttctgctattccatctctgatatgcgattggcattctactagaaaattatattgaaactgactcatttcatctca-acagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA

upper sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------------------------------------------------caaagttggaatttgattatgtcg------taaaatatatgcaccc-tacatgttt-tagcttcatattgacttatattt-tcatatgtgctccttcaactgcacaaa--------------gCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
                                                                            || |    | |||    ||  |        ||   || |  ||| |  |||       || | |||||  |   |||| | | |  |    || ||  |    | |||              | | ||||| |||||| ||||||| |||||||| |||||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||| |||||||| || |
gtattagtgacttgctttcattgtttgtgtccaactaatttattctttgggatgaatgcctccagtttttggagtgcagatcatgcattcatctaccttaacctgttattttacacacacacacacacacacacagatgcatatgcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctcttgccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA

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|29659877|gb|CB656152.1|CB656152
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33675353|gb|CF303592.1|CF303592
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58688253|gb|CK076940.1|CK076940
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58688764|gb|CK077451.1|CK077451
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29631643|gb|CB636652.1|CB636652
EST:     AACTCCATCATGAGCTACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29678221|gb|CB674496.1|CB674496
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33676336|gb|CF304575.1|CF304575
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58687558|gb|CK076245.1|CK076245
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCAC
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCAC
EST: gi|29635195|gb|CB640204.1|CB640204
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29662456|gb|CB658731.1|CB658731
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58606034|gb|CK034067.1|CK034067
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29683422|gb|CB679697.1|CB679697
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29664618|gb|CB660893.1|CB660893
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58605455|gb|CK033488.1|CK033488
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29657250|gb|CB653525.1|CB653525
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33799165|gb|CF325440.1|CF325440
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33801382|gb|CF326562.1|CF326562
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|33798134|gb|CF324927.1|CF324927
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29623544|gb|CB628555.1|CB628555
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|29658233|gb|CB654508.1|CB654508
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
EST: gi|58695779|gb|CK084466.1|CK084466
EST:     AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAG                         CTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT
genomic: AACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtg ... ctgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttagcttcatattgacttatattttcatatgtgctccttcaactgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
            tattgac  putative branch site (score: 2)
           atattgacttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaagttggaatttgattatgtcgtaaaatatatgcaccctacatgttttagcttcatattgacttatattttcatatgtgctccttcaactgcacaaagCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - atatgca
- - - - - - - - - - - - - - - - - - -ccctaca
- - - - - - - - - - - - - - - - - - - - - - - - - -gcttcat