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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtgttgtattatttgataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC

Basic information

species Oryza sativa
transcript LOC_Os04g59040.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G061928_T02 (Zea mays), 3'ss of exon 4
ctgtgttgtattatttgataggtc--tgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
 | ||||  || || ||  |||    | || |  | | |||  | | | || |  | | |    |  ||   |  || | ||  ||    | ||||||| |||| || || ||||| |||||||||||||| || || || |||||||||||| |||||||||| ||||||||||||||||| |||||||||||  | ||||
-tctgttacataatctgtcaggctgattcagtcctgaactgatgaaatgtaatggtttaatttgactttctttcgttctgac-atgtgctacaatttgatagGTTGATCGAGTCCTGTACTCATCAGTTGTATACCCTCACAATTATGGTTTCGTTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTAGTCC

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 4
ctgtgttgtattatttgataggtctgc--atttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
 ||||||  || |||||  |||       | || |  ||||  | | | || |  | | |     | ||   | ||| ||||  |   | | |||||||||||| || || ||||| |||||||||||||| || || || ||||||||||||||||||||||| ||||||||||||||||| |||||||||||  ||||||
-tgtgttacataatttgtcaggatgattgagttctgtgctgatgaaatgtaatagtttaatttgtttttctttctttctaacctttgct-acaatttgacagGTTGATCGAGTCCTTTACTCATCAGTTGTATACCCTCACAATTATGGTTTCATTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTGGTCC

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
----------------------ctgtgttgtattatttgataggtctgcatttgta-agctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatt---tgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
                      ||||  || |     | |  | | |   ||   | || | |   || | ||| || ||  | |    |  || ||| |   |  | ||  | | |   | |||||| || || ||  | || ||||||||||| ||||| ||||| |||||||| || ||  | ||||| |||||||||||||||||||| |||||| |||| |
gtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G18510.1 (Glycine max), 3'ss of exon 3
----------------------ctgtgttgtattatttgataggtctgcatttg--taagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatt---tgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
                      |||   || |       |  | | |   ||     ||  | |     |   || ||  |  | |    |  || ||| |   |  | ||  | | |   | |||||| || || ||  | || |||||| |||| |||||  |||| |||||||| || ||  | ||||| |||||||||||||||||||| |||||| |||| |
gtacaaaccaattacctggttactggaatggaagcccctactgctatatcttgaaacaaattttccagatgattttttcccccatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCATTTGTTTATCCATATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
-----ctgtgttgtattatttgataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
      ||  || |   || |      |  ||| || | |  ||| |  |    | || ||| |     |||| ||| || | ||  |   | || | | | ||||| || || ||  | |||||||||||||| ||||| ||||| ||||||||||| ||||| || || |||||||||||||||||||| |||||  |||| |
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtcta---tcattatattcttcttacctt--ctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 4
----------ctgtgttgtattatttgat---aggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
             ||     ||||| ||    | ||||  | ||    ||   | || ||  ||| | |  |   || |  | || |  | ||  |  |  |  | || | |||| || || ||  | || ||||||||||| ||||| ||||| |||||||| || ||  | ||||| |||||||||||||||||||| |||||| |||| |
gtacaaaaccaattgcctggttattggaattgaagtctctacttact-gccaaatgatttgtttcctat--acacatctatctttatgcttacgattttcgaataattcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------------------ctgtgttgtattatttgataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
                                                                           |  || || |  || || |   ||| |  || |    |||| |  |   ||| | | |  | |    |  |||||   | |||    ||| | |   ||||||||||||||| |||| ||||| || |||||||| ||||| ||||| ||||||||  | || || |||||||||||||||||| |||||||| |  |||
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggag-atctgttttttcttccattttgttatgtatgcatgccttcatatgatggga----atgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 4
--------ctgtgttgtattattt---gataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
         |   |||    ||||    |  ||| ||    || | | ||  |   | ||| ||       ||    | |||| || | |   |      |   |   ||||| || ||| |||||||||| || || ||||| || || |||||||||||||||||| | || ||||| || ||| | ||||| || |||||||||||| 
gtgaatgtttagattgggagatttctgaaggggtttggtaatgcatgttgacgagatgtatgctgtgtttcgaccgct-cattgttctgaacat---cggttgctctgcagGTGGATCGTATCCTATACTCGTCTGTGGTGTACCCGCACAATTATGGTTTCATTCCACGCACCCTTTGCGAGGACGAGGATCCCATCGATGTTCTGGTCA

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
ctgtgttgtattatttgataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgt-gcttcataatttga-----------cagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
       |||     |     ||    |  | ||| |  |      ||  | |  |||     | ||   ||     |||    ||| | |||| | |           ||||| || ||| || | |||||||||||||| ||||| || |||||||| ||||||||| | || |||||||| ||  | ||||| || |||||||| ||| 
-------gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA

upper sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 1
--------ctgtgttgtattattt---gataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
         |   |||    ||||    |  ||| ||    || | | ||  |   | ||| ||       ||    | |||| || | |   |      |   |   ||||| || ||| |||||||||| || || ||||| || || |||||||||||||||||| | || ||||| || ||| | ||||| || |||||||||||| 
gtgaatgtttagattgggagatttctgaaggggtttggtaatgcatgttgacgagatgtatgctgtgtttcgaccgct-cattgttctgaacat---cggttgctgtgcagGTGGATCGTATCCTATACTCGTCTGTGGTGTACCCGCACAATTATGGTTTCATTCCACGCACCCTTTGCGAGGACGAGGATCCCATCGATGTTCTGGTCA

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|33684219|gb|CF312458.1|CF312458
EST:     TATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: TATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
EST: gi|87023771|gb|CI288124.1|CI288124
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
EST: gi|88732604|gb|CI755781.1|CI755781
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATT
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATT
EST: gi|86848615|gb|CI293930.1|CI293930
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
EST: gi|2309908|gb|C26063.1|C26063
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGGTTT
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGG-TTT
EST: gi|88721865|gb|CI743377.1|CI743377
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
EST: gi|286879|gb|D15686.1|D15686
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTTCCTATACTCATCAGTTGTGTAT
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGT-CCTATACTCATCAGTTGTGTAT
EST: gi|88726501|gb|CI750156.1|CI750156
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCCATAATTATGGTTT
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCC-ATAATTATGGTTT
EST: gi|33684220|gb|CF312459.1|CF312459
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
EST: gi|86907275|gb|CI292840.1|CI292840
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
EST: gi|88423146|gb|CI613447.1|CI613447
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
EST: gi|88742766|gb|CI766274.1|CI766274
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTT
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTT
EST: gi|88405920|gb|CI591315.1|CI591315
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
EST: gi|88427290|gb|CI586838.1|CI586838
EST:     AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
EST: gi|163925905|gb|EG712281.1|EG712281
EST:     AGGGAAGCAAAGCGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG                         GTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC
genomic: AGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAGgtgtgtgttc ... aatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
                            ttgtaac  putative branch site (score: 2)
            aaagaatattacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtgttgtattatttgataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA