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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaatctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT

Basic information

species Oryza sativa
transcript LOC_Os08g25734.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaatctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                                                                    || |||  ||          |  |  ||  |   | |       ||     | |||        |     ||    ||||||   ||||||||||   ||||||| || |||||  |||||||||||||||||||||| || |||||||||| |||||| |||||||||||  |||||||||| || |||||  |||||||||
----------------------------------------------------------------------------------agcttactagaaagcctaggcaggttgggttgtc--tcaaggcaggatggaaggaagggttgcctttcagaatggaatttaagaccttatttttgtt---tgcagGTTCAGGCTTATCTGTATGATGGTTACTGGGAAGATATCGGTACCATTGCGGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAATACCAGATT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtagg-tcatgtgctatatt-tgctgcttaagaatctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                                                                    |   ||  ||          |  |  ||  |   | |       |      | ||| | |     | ||   || |  ||||||   |||||||   |||||||||| || |||||  | ||||||||||| |||||||| |||||||| ||||||||||| |||||||||||  |||||||||| || |||||  |||||||||
------------------------------------------------------------------------------------catgctagaaagcctaggcaggttgggt--tggctcaaggccggagggagggaagggttacaccttttaaaatggtatttaagaccttattttt---gtctgcagGTTCAGGCTTATCTATATGATGGTTATTGGGAAGATATTGGTACAATTGAGGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAATACCAGATT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttga-ccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgc-tgcttaagaatctatttttgt-tgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                                                      | || ||  ||||||     |  ||||||   |   | |   |   |  ||  |   |    |  | |||  ||||   | | || |  || |  |     | ||| ||| | |   ||||| |||||||||||||||||||| |||||||||||||||||||| |||||||| ||||||||||||||||||||||| || ||||||||||| || || |
----------------------------------------------------------------------gtatgtgttccttctggttatttaatattacgaaaactttcttgtcattttcttgcatagcaaaatttag--catgcaattttttagaatgttgtatggcatgtttgtgtatattcacagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattactt---------gtaggtca-tgtgctatatttgctgcttaagaatc-tatttttgt---tgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
    |  |  |  | ||                                                                                                    |  ||||| || ||| ||         |||  | |   ||| || |||   |  || | |    || |||||   | |   ||||| |||||||||||||||||||| |||||||||||||||||||| || ||||| ||||||||||||||||||||||| || ||||||||||| || || |
----gtgattcctggtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaactttcttgttattttcctgcatggtaaattagcatgcaattttttgagaatatgtacggcatgtttgtgtgtattcacagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATCGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttt-tatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaa-tctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                     ||     ||| | ||| |  |||||  ||  ||  ||| |||  |  |   ||    |   ||| | |||    ||| ||  | || |  | | | ||   ||| ||   ||  ||    |  | |||   |       | |   || | |  |  ||    |||||||| ||||||||| | ||||||||||||||||||||||||||||| || |||||||| ||||| || ||||| ||||| || || || || || || ||||
---------------------gtgagtgtttatattcat--gtttacaacatctagtttgtattctgatgctcaagcaagtctctgttact---ctatggt--ttgctttcggattcaacagcttctt--gtagctgattatgctatgcagaaggcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaatctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                                                                |    |||||| || |||   ||         || |  ||| ||| |    | |||    || |  |  |  |||  |       |||   |   |  | |||| |||| |||||||||||||||||||| |||||||||||||||||||| |||||||| || ||||| || ||| |||| || || || ||||| || |||||||
--------------------------------------------------------------------------------tatgatcactggaa-attccgataat-----caaaatgttattttatctgcatttgcct-tcttaagagaactttcatagagtcaaattgctgcataatctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaatctatttttgttgtctg-cagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                                               |  || ||| | |||  |||   ||   ||     | ||| | |   |||||||||         | || ||||| || |||| |             | ||||  | ||| |  ||| |  ||||| |||||||| ||||| ||||| ||||||||||| ||||| || ||||| |||||||| ||||| |||||||| || || || || ||||| || ||||
-------------------------------------------------------------gtagggtgagc-tgtgaatttc---catacaacctcagccattgga--ggtaataaat---------agtagttgtacgtaatgttcc------------tgagaagatttttgttctgtttatcagGTTCAAGCTTATTTGTACGATGGCTACTGGGAAGATATTGGAACTATTGAAGCATTCTACAATGCCAATCTGGGCATCACTAAGAAACCTGTTCCTGATT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaatctatttttgttgtctgc-agGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                                                                        | || ||||   ||  |  | | |   ||  |  | ||   |  |       | |   ||  | ||  |   |    | | |   |   |||| | | |||| ||||| |||||||||||||| |||||||||||||| ||||| || ||||| ||||| || || ||| |||| || || || ||||| || |||||||
---------------------------------------------------------------------------------gaatattcggagatatctccaaaggttgtctgtgaacgtgatgttcagtggc-----aatgacccgcattgttcccaatt--gtattgtgactggattgtgtaccagGTTCAAGCGTACTTGTATGATGGCTACTGGGAAGACATCGGTACTATCGAGGCTTTCTACAACGCGAATTTGGGCATCACCAAGAAGCCCGTGCCAGATT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaatctatttttg--ttgt-ctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                                                                       | ||||| | | || |    |         |  |  |     | | | | |    |||  |  || ||       |   || |  || |   | ||  | ||||| ||||| ||||||||||| || ||||||||||| ||||| || || || || ||||| ||||||||  | || || ||||| |||||||| || || |
-------------------------------------------------------------------------------------gtattgaaa-actttcgtaaggtccactcccgaaaatgtgaccgtcattggca----atggccagtacttttcctagagatatttgattctaaatcgtattccagGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ16157 (Selaginella moellendorffii), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaatctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                                                                                                          ||| || || ||   | |  ||  |  |     |   |||||  |      | ||||   ||||||| ||||| || ||||||||||| |||||||||||||| || || || |||||||| ||  |||| ||  | ||| | || || ||||| || ||| | |
-------------------------------------------------------------------------------------------------------------------------gtttgtttttgctctgaagggat-cgaaacgaacgtgacttaaacaata--ctctgttcgttgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ17026 (Selaginella moellendorffii), 3'ss of exon 4
gtatggaaagctcgctgtttagtagccttttgttttcttcagtttattactgctgcttttatgattgttagcatttgaccttctctcactgaaatattgtcatggcatatgtaataaattacttttttattacttgtaggtcatgtgctatatttgctgcttaagaatctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                                                                                                          ||| || || ||   | |  ||  |  |     |   |||||  |      | ||||    |||||| ||||| || ||||||||||| |||||||||||||| || || || |||||||| ||  |||| ||  | ||| | || || ||||| || ||| | |
-------------------------------------------------------------------------------------------------------------------------gtttgtttttgctctgaagggat-cgaaacgaacgtgacttaaacaatg--ctctgttcgtcgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

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|13420424|gb|AU174514.1|AU174514
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|87012877|gb|CI297104.1|CI297104
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|58606969|gb|CK035002.1|CK035002
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTAGAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|33681770|gb|CF310009.1|CF310009
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|58678083|gb|CK066770.1|CK066770
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|88586416|gb|CI704115.1|CI704115
EST:     TGACTTTGGAAGTGAAGTCATTCCAGGTGCCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: TGACTTTGGAAGTGAAGTCATTCCAGGTGC-AACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|29614233|gb|CB619246.1|CB619246
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|58652879|gb|CK041559.1|CK041559
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|58675386|gb|CK064073.1|CK064073
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|88584775|gb|CI702352.1|CI702352
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGAAATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|86831383|gb|CI299441.1|CI299441
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
EST: gi|29681248|gb|CB677523.1|CB677523
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGNGAAGACATTGGTACCA
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCA
EST: gi|29620180|gb|CB625192.1|CB625192
EST:     ATGAC-TTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 702

TAGTAAAAATGTAATGCTTCAGCTCCTCCGTGAACAATTTCCTGGAGCTAATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtaggtcatgtgctatatttgctgcttaagaatctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                       tttttgtt  CT-rich tract
                            ttaagaatctattttt  TA-rich tract