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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcacgcatcacatcccgtttgatcaattcaaccacattttctgcaccaaattaactcgtttgaaaatgcgtgaaatttacggggttgtgtatgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC

Basic information

species Oryza sativa
transcript LOC_Os03g56110.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g56110.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G135447_T01 (Zea mays), 3'ss of exon 4
------------gtacgcacgcatcacatcccgtttgatcaattcaaccacattttctgcaccaaattaactcgtttgaaaatgcgtgaaatttacgggg-------------ttgtgta-tgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
             || |    | ||    |  |  |    ||| ||||  ||  | |||   | |  |         |||||    ||||  ||  |  |             | | ||| | | ||||||| |||||||||| |||| ||  ||||||| |||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||| || 
gtaagaccctacctatgtttccttccatccatgcattgctaatacaacggcaactactgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatgactactgtttcgagtactcaccagGAGACGGAGAAGATGGCGCTCGCAGAGACGACCGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT

upper sequence: LOC_Os03g56110.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G10430.1 (Glycine max), 3'ss of exon 4
--gtacgcacgcatcacatcccgtttgatcaattcaaccacattttctgcaccaaattaactcgtttgaaaatgcgtgaaatttacggggttgtgtatgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
  | |  ||| |||   |     ||  || ||||    || || |  |  |   |  ||  ||  |  ||| |  ||     | | || | |   ||   | ||||    |||||| || |  ||||  |  | || ||  ||||||| ||||| || || ||||||||||| |||||||||||| |||| ||||| ||  |  
gtgaaaccacacatt-tacaattttcaataaattttgtcatatgtgtttgatatatatatttc--taaaaattatgtacttctcatggtggtcactact-gtagGAATCAGAGAAGGTGGCATTGGCTGAATCAACTGGTTTGGACCAAAAGCAAATAAATAACTGGTTCATAAACCAGAGGAAGAGGCATTGGAAACCATCTG

upper sequence: LOC_Os03g56110.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
---------------------------------gtacgcacgcatcacatcccgtttgatcaattcaaccacattttctgcaccaaattaactcgtttgaaaa------tgcgtgaaatttacggggttgtgtatgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
                                  |  |      || | |   |  |  |        |     ||| | |      |     | ||| |         |   ||| |||| |   ||||||  ||  |||||||   | |||  ||  || |||||  | || ||||||||||  |||||||||||||||||||| || |||||| | |||||||||||||| |||  | 
gtgagtacctttgtgttctttcttgttggcattctgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcatcgcttttttctttgacatttgcttcgttgtgc-tggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG

upper sequence: LOC_Os03g56110.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
------------------------gtacgca---cgcatcacatcc-cgtt-tgatcaattcaaccacatt--ttctgcaccaaattaactcgtttgaaaatgcgt--------gaaatttacggggttgtgtatgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
                        ||  |||   ||  || | | | |||| ||   | |       |  |   | ||  ||   ||       ||   | ||| |        || |||| |   | ||||  ||  |||||||   | |||  ||  || |||||  | || || |||||||  |||||||||||||||||||| || |||||| | |||||||||||||| ||   | 
gtgagtacctttgtgttctttcttgttggcattccgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcattgcttttttctttgacatttgcttcgctgtgc-tggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG

upper sequence: LOC_Os03g56110.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ07541 (Selaginella moellendorffii), 3'ss of exon 5
gtacgcacgcatcacatcccgtttgatcaattcaaccacattttctgcaccaaattaactcgtttgaaaatgcgtgaaatttacggggttgtgtatgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
                                       || || || |     || | |   || | | |    |   |||    ||||    | || |||||||     ||| | ||   |   | ||  || || || ||||||||||| || ||||||||||| ||||||||||| ||||| || ||||| ||  |  
-------------------------------------gtatgttgtg-atagttttcattgaatttatattcttagttgtttggctggtttc--agGAACAGGAGA-----AAGCTAACCTCGCAACTGAT-ACTGGACTCGACCAGAAGCAAATTAACAACTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG

upper sequence: LOC_Os03g56110.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ10744 (Selaginella moellendorffii), 3'ss of exon 5
gtacgcacgcatcacatcccgtttgatcaattcaaccacattttctgcaccaaattaactcgtttgaaaatgcgtgaaatttacggggttgtgtatgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
                                       || || || |     || | |   || | | |    |   |||    ||||    | || |||||||     ||| | ||   |   | ||  || || || ||||||||||| || ||||| ||||| ||||||||||| ||||| || ||||| ||  |  
-------------------------------------gtatgttgtg-atagttttcattgaatttatattcttagttgtttggctggtttc--agGAACAGGAGA-----AAGCTAACCTCGCAACTGAT-ACTGGACTCGACCAGAAGCAAATTAACAATTGGTTTATCAACCAGAGAAAGCGTCATTGGAATCCTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccaaattaactcgtttgaaaatgcgtgaaatttacggggttgtgtatgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC
     aattaac  putative branch site (score: 2)
               tttgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcacgcatcacatcccgtttgatcaattcaaccacattttctgcaccaaattaactcgtttgaaaatgcgtgaaatttacggggttgtgtatgagcagGAGATGGAGAAGATGACGCTGGCGCAGACGACGGGGCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGCGGCACTGGAAGCCGACGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG