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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatggatcaatgctctcctttccctgttagattacgccaaattctagtttaaggttcgcatccgtgttgttagtattgcggttttatagtgagttt...

Basic information

species Oryza sativa
transcript LOC_Os01g16890.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16890.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G027728_T01 (Zea mays), 5'ss of exon 2
TCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatggatcaat---gctctcctttccctgttagattacgccaaattctagtttaaggttcgcatccgtgttgttagtattgcggttttatagtgagttt
||||||||||||||||| |||||||||||||| || |||||||| ||||||||||| |||||||||||||||||||||||||| ||||||||||| ||| |||||     ||  |   ||  |  | |    | |||       | ||   |         | | |||  | ||   | | | |    || | | |  ||   
TCCACGGACAACATCAATAACAAGCTGCAGCTTGTTATGAAGAGTGGCAAGTACACTCTCGGCTACAAGACCGTCCTCAGGACTCTCAGGAACTCTAAGTgtaagtcatttctttcaagcaataatgtttgcggtagggcctttcgaagcatgtgaattcatgcacatttg-gtaagtcgcagtttaattctttggcaaga--

upper sequence: LOC_Os01g16890.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G050460_T02 (Zea mays), 5'ss of exon 2
TCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatggatca-atgctctcctttccctgttagattacgccaaattctagtttaaggttcgcat-ccgtgttgttagtattgcggttttata-gtgagttt
|||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| || ||| |||||   | ||| |   | |  | |  ||  |   | | || |     ||| |   | ||  |       || || |     | |  | |  | ||  |  |
TCCACGGACAACATCAACAACAAGCTTCAGCTTGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACTGTCCTCAGGACCCTCAGGAATTCTAAGTgtaaggaagctcacactttatattctgtctcatgcgtaaggcta---cttagctcttgattaacgggttaggtagtcaaatcggtgcatatggatgtctgcct

upper sequence: LOC_Os01g16890.3 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
TCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatggatcaatgctctcctttccctgtta--gattacgccaaattcta-gtttaaggttcgcatccgtgttgttagtattgcg----gttttatagtgagttt-----------
 |    || |||||||||||||||||    |||||||||||||||||||||||||||||||||||||||||||| |||| || |||||| | ||||||||||  | |  |    |  |     ||    | ||  |||     |   |  |   |||  |||  |  |  |  |||| | ||| |      |||||         ||           
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttctcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag

upper sequence: LOC_Os01g16890.3 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 5'ss of exon 2
TCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgg-atcaatgctctcctttccctgttag-attacgccaaattctagtttaaggttcgcatccgtgttgttagtattgcggttttatagtgagttt------------------------------------------------------------
 ||  ||| |||||||||  |   |||  ||| ||||||||||| ||||||||||| || ||||||||||||  ||| | ||||||  |      |||||||||| | |       ||   |     ||   | |   | |  |||     |      |   |   | |    |||  |  |         |   ||  ||                                                             
ACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGGGCAAGGgtaagtttgcgctcgcgccgacgcccgccgactggtgcttcctcaacccgcaccccctgccccttgtgccctgtgtggggctcagcaccgcacgctgccttctccaccagaaaactgcacatctatctcaccaactttgtctcctcttcttgcccaccgcag

upper sequence: LOC_Os01g16890.3 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ14031 (Selaginella moellendorffii), 5'ss of exon 1
TCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatggatcaatgctctcctttccctgttagattacgccaaattctagtttaaggttcgcatccgtgttgttagtattgcggttttatagtgagttt
 ||  ||| | |||||||||||   ||  ||| |||||||||||||||||||||||||| ||||||||||| || ||||   | ||  | |       ||  ||| ||    |   ||||   || |   |  ||||   |||  ||   |  |  ||| ||||                                    
ACCCAGGAGAGCATCAACAACAGATTGGCGCTGGTGATGAAGAGCGGCAAGTACACGCTGGGCTACAAGACGGTGCTCAAATCGCTGCGCAGT-----GGAAAAGgtgtgaaatccctctttgtttctcttgcgattgatcca--ttggcgcattgggtgcgcag-----------------------------------

upper sequence: LOC_Os01g16890.3 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ13021 (Selaginella moellendorffii), 5'ss of exon 1
TCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatggatcaatgctctcctttccctgttagattacgccaaattctagtttaaggttcgcatccgtgttgttagtattgcggttttatagtgagttt
 ||  ||| | |||||||||||   ||  ||| |||||||||||||||||||||||||| || |||||||| || ||||   | ||  |||     || |||  |    |||    ||||   || |   |  ||||   |||   |   |  |  ||| ||||                                    
ACCCAGGAGAGCATCAACAACAGATTGGCGCTGGTGATGAAGAGCGGCAAGTACACGCTGGGGTACAAGACGGTGCTCAAATCGCTGCGGAGTGGAAAAGgtgtgtgaaatc---cctctttgtttctcttgcgattgatccag--tggcgcattgggtgcgcag-----------------------------------

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|88736230|gb|CI759738.1|CI759738
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88302833|gb|CI668679.1|CI668679
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88350047|gb|CI621978.1|CI621978
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88580500|gb|CI697434.1|CI697434
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88331484|gb|CI675819.1|CI675819
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88347491|gb|CI637431.1|CI637431
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88593163|gb|CI711321.1|CI711321
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88305970|gb|CI634967.1|CI634967
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88591785|gb|CI709839.1|CI709839
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88761833|gb|CI771389.1|CI771389
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88588610|gb|CI706439.1|CI706439
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88570474|gb|CI661847.1|CI661847
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|86900722|gb|CI302139.1|CI302139
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88405170|gb|CI685624.1|CI685624
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|86889679|gb|CI299877.1|CI299877
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88763053|gb|CI772609.1|CI772609
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|55413584|gb|CV725960.1|CV725960
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
EST: gi|88572868|gb|CI664439.1|CI664439
EST:     GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGG                         CGAAGCTATTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA
genomic: GTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatgga ... ttcattacagCGAAGCTAGTGATCATTTCTAACAACTGCCCACCTCTTCGGAAGTCAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCACGGACAACATCAACAACAAGCTGCAGCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTCCTCAGGACCCTCAGGAACTCCAAGGgtaagatggatcaatgctctcctttccctgttagattacgccaaattctagtttaaggttcgcatccgtgttgttagtattgcggttttatagtgagttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctttccc