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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcttcagcattggtggcatcattttcccatacagttctagatatttacatatgattttaaattgttaacatatcttaattgctatgatttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC

Basic information

species Oryza sativa
transcript LOC_Os03g50850.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
agcttcagcattggtggcatcattttcccatacagttctagatatttacatatgattttaaattgttaacatatcttaattgctatg-----atttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC
  |   |  ||    |||| | |||||   ||   ||    |  | ||      | |||   || | |     | |||| || ||||     ||  |||  |||||||||||| |||||||||||||||||||| ||||| ||||||||| ||||||||||||| ||||||||||| ||||| |||||||| |||||||| || |
-accagaaaatcaa-ggcacctttttcttttatgcttagtaagctcta---gcaaatttgttttctgatgcatttttaactgttatggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC

upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA06G13290.1 (Glycine max), 3'ss of exon 10
agcttcagcattggtggcatcattttcccatacagttctagatat-ttacatatgattttaaattgttaaca-tatcttaattgcta-------tgatttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC
           |       | |  |    | |  | |   ||  | ||  ||| |||| |  || | | ||| ||| || ||   ||       | || | | | ||||||||| || ||||||||||| || ||| |||| || |||||||| |||||||  || || ||||| || || ||||||||||| || |||||||| ||||
---------gataaatctgttaactgattaaaagggtagggacttgttgtataggattctttatggctcacagtattttgatcattaaataatataatatgtatttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC

upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 10
agcttcagcattggtggcatcattttcccatacagttctagatatttaca-tatgattttaaattgttaaca-tatct-------taattgctatgatttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC
         ||   |    | |       | |  || |    |  ||| | || |||| |  || | | ||| ||| |       ||| |  ||| || | ||| ||||||||| || ||||||||||| || ||| |||| || |||||||| |||||||  || || ||||| || || ||||||||||| || |||||||| ||||
---------ataaatctgttgacccattaaaagggtacggacttgttatagtaggattctttatggctcacaatatttggatcattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC

upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 10
agcttcagcattggtggcatcattttcccatacagttctagatatttacatatgattttaaattgttaacat--atcttaattgctatgatttttt--tgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC
 |||   |   |    |    |    ||  |  ||||     | |      |  ||| | ||| |     ||  |  || |   ||    ||||||  | |||||||||||| |||||||||||||| || ||||| |||||||||||  |||||| |||||||||||| ||||| |||||||||||||| || ||||| || |
-gctat-gtgctaactgagaaagaagccattggagttt--actttggggggacaattgtgaatagcctctatggactttgaagactgcttttttttaatttcagGAATTCAAGTGTGAGATATGTGGGAATCACAGTTACTGGGGGCGTAGGGCTTTTGAGCGGCATTTTAAGGAATGGCGCCATCAGCATGGTATGCGTTGCC

upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S218_51V6.1 (Physcomitrella patens), 3'ss of exon 10
----agcttcagcattggtggcatcattttcccatacagttctagatatttacatatgattttaaattgttaacatatcttaattgctatgatttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC
    |   |  ||  | |        ||      | ||||    ||   |  | | |   |   |  | |      | ||  ||||    |   |  || |||||| || |||||||||||||| || ||  | ||||| ||||| |||||||||| ||| || || |||||||| ||| | |||||||| || ||||| ||| 
taagacgcttggccgtagaaatgaatttcggttctgcagtgtaggaccatctcttttttctcgcagcttt----gcacctggattgacgagtgataattttcagGAGTTTAAATGTGAGATATGCGGCAATTATAGCTATTGGGGTCGACGGGCTTTTGAACGACACTTCAAGGAATGGAGACATCAGCATGGAATGCGTTGTT

upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ22878 (Selaginella moellendorffii), 3'ss of exon 9
agcttcagcattggtggcatcattttcccatacagttctagatatttacatatgattttaaattgttaacatatcttaat-tgctatgatttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC
                                             | | |  | ||  |   |  ||  ||   ||| || | || |  ||| |||  ||||| |||||||| |||||||||||||||  |||||||||||||||| |||| |  || || || ||||| || ||| | ||||||||||| ||||||||  
--------------------------------------------gtaaaaagttatgctccttcttttgcaagccttcatctcctctcctttgttttgcagGAGTTCAAATGCGAGATATGTGGAAACTCCAGCTACTGGGGGCGAAGGGCCTTCGAACGACACTTCAAAGAATGGAGGCATCAGCACGGCATGCGCTGCT

upper sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ30765 (Selaginella moellendorffii), 3'ss of exon 9
agcttcagcattggtggcatcattttcccatacagttctagatatttacatatgattttaaattgttaacatatcttaattgctatgatttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC
                                      || | | |||       | ||   ||| |  |     | |  | || |  ||| |||  ||||| |||||||| |||||||||||||||   ||||||||||||||| |||| |  || || || ||||| || ||| | ||||||||||| ||||||||  
-------------------------------------gtaaaaagttattctccttctt---ttgctggc---cgtcatctcctctcctttgttttgcagGAGTTCAAATGCGAGATATGTGGAAACTCTAGCTACTGGGGGCGAAGGGCCTTCGAACGACACTTCAAAGAATGGAGGCATCAGCACGGCATGCGCTGCT

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|25806388|gb|CA762349.1|CA762349
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|58030390|gb|CX727933.1|CX727933
EST:     GCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: GCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|88966922|gb|CI379806.1|CI379806
EST:     TATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGATATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: TATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|58030389|gb|CX727932.1|CX727932
EST:     GCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: GCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|87039441|gb|CI194063.1|CI194063
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|58683962|gb|CK072649.1|CK072649
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29625135|gb|CB630146.1|CB630146
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29664559|gb|CB660834.1|CB660834
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|86602502|gb|CI264830.1|CI264830
EST:     ATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29675683|gb|CB671958.1|CB671958
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29664555|gb|CB660830.1|CB660830
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|88228807|gb|CI226658.1|CI226658
EST:     ATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|58674178|gb|CK062864.1|CK062864
EST:     ATAAGCTCCATGGTCTTGG-CAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29639904|gb|CB644913.1|CB644913
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29629058|gb|CB634069.1|CB634069
EST:     GGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: GGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|86253465|gb|CI058390.1|CI058390
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatatgattttaaattgttaacatatcttaattgctatgatttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC
                                           tttttttgtc  CT-rich tract
     tatgattttaaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcttcagcattggtggcatcattttcccatacagttctagatatttacatatgattttaaattgttaacatatcttaattgctatgatttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- cttcagc
- - - - - -tggtggc
- - - - - - - - - - - - - -ccataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctatg