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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_Os08g25734.2
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|29681248|gb|CB677523.1|CB677523
EST:     ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGNGAAGACATTGGTACCA
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCA
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|29620180|gb|CB625192.1|CB625192
EST:     ATGAC-TTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGG                         GTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG
genomic: ATGACTTTGGAAGTGAAGTCATTCCAGGTGCAACAAACATCGGAATGAGGgtatggaaag ... ttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtaggtcatgtgctatatttgctgcttaagaatctatttttgttgtctgcagGTACAAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATT
                                       tttttgtt  CT-rich tract
                            ttaagaatctattttt  TA-rich tract