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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG

Basic information

species Zea mays
transcript GRMZM2G140328_T02
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                           ||||    |  |||   ||  | | |  ||||  || | | || ||   |||     |||||||| || |||  | | ||  |  |||   ||  |||||  |   |||||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||||
----------------------------------------------------------gtttatctctcgact---aatgttccatcatgtt-ttgaaagaaacaatcttc-----atgttcaacaaccataatccagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                         |||| | |  | |     || | |||   | ||    ||||  | || ||||  ||        | ||| ||  | ||||                    | || | |  | | |  |  ||  |||| |||||||||||  ||||||| || || || || |||||||| || ||||| |||||||| ||||| |||||||||||||| || ||||| |||| |
-----------------------------------------ctattaga--atctattgttcagacacacattttttggttcaaattaggtaaactagtt---tttgttttcatggttgttt-------------------ttgtgactctatttttgagttt--agGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 27
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                            ||     | |   ||||  |  |||||||  || | |  |  |  |   |  | ||||  |    |    |  |   ||  |  ||| |  | | || |  ||  |||||||||||||||| || ||||||||    |||||||||||||| || || || || |||||||| ||| | || ||||| || |||||||| || | |
-----------------------------------------------------------attggttgtcatgctccat-tctctaatattaaaataattcctgt-ttactaaaaagatccttgttatagttaatcttgtgct--ttact--attttgta--ttttagGCAGATATTGGTCTTTCTATGGGCATCTCCGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGACAACTTTGCATCAGTAGTAAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttg------cagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                                      |  |    | |  | || |   |||||   ||  |  |       | |    || ||| |||||    ||||   |   |  || |   | ||        |||| ||||||||||| || |||||||| || |||||||||||||| || || || || |||||||| ||| | || || || || |||||||| || | |
---------------------------------------------------------------------catctgtttggttgtcatgttccatttattaaaataattcct----gtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                                  || |   || |   | || | |  |  |||     |   | | |  ||   | ||       |||  ||  ||  | || | |  | | |   | ||  |||| |||||||||||  ||||||| || || || || |||||||| || ||||| |||||||| ||||| |||||||||||||| || ||||| |||| |
---------------------------------------------------------------tctattagaatctattgttctgacacattttttggttcaaattatgtgaactagtttttgtttt-catggtt--gtgtttgtgactctatttttggagtt-tagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 24
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagtta-atgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                           |  |    ||||||  ||   | | |||    |  ||         |  |    |||      |      ||  ||   | ||| ||  ||  | | |   | |   |||| ||||| |||||| ||||||| || || || || ||||||||||| ||||| || ||||| ||||| |||||||||||||| || ||||| |||| |
-----------------------------------------------------------taaaggtttgaactatca---ttccaatgcagatgtttt-----tgttctaatgcagtaaactagcttttattcttttcttgtaattctatacatttttggaat-atagGCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 26
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                              |||  |||| ||  || ||| | || |  ||  || |         ||  |   || | |       |  ||     |||  || |  |  | || || ||  |||||||||||||||| || |||||||| || ||||| |||||||| || || ||||| |||||||| ||||||||||| || || |||||||| || | |
--------------------------------------------------------------aaagttgaaatttaaaattcattat-taaaacctagagtttatcaattatattaatttccttattatag-ttgatacagtgctttacta-ttatgtaattt--agGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 24
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcc-tcattttaa-acatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                             |    || |  |||||| ||  || ||  ||      | ||||  |||| |  ||  ||  | ||||       | |||        | |||  ||| |  |  ||  | | || ||  |  |||| ||||| |||||  ||||||| || || || || ||||||||||| ||||| |||||||| ||||| |||||||||||||| || ||||| |||| |
--------------------------------------------aggtttgaactatcatttcaatgcaggagtttttg---ttctaa--tgtagtaaac-taactagcttt-------tattc--------tgtttttgtaat--tctatacattttggaa--tatagGCCGATATAGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 26
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                             | | | |  |  |   |  | || ||||     |   | || |||||||||     | ||| |||  |     ||| |   |   | || |  |              | || || ||  |||||||||||||||| || |||||||| || ||||| |||||||| || || ||||| |||||||| ||||||||||| || || |||||||| || | |
-------------------------------------------gggtaccaaatccgaaactggaaataaact----gggatcaaaaatgtaatttt----accatttttttattatagtttatacaatgttttactat--------------tatgtaattt--agGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 24
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                                         || ||       | | || || ||   | |  |  |    |  || | |||     || ||||  | || |        || || |   |  |||||||||| ||||| || ||||| ||    |||||||||||||| || ||||||||||| || ||||| |||||||||||||| || ||||| || | |
---------------------------------------------------------------------gttctctaacaattctacaggttatgtat-tatgtgttgtgtgtc--atctccaaatctgatttttcttttgttg--------ctttgga--ctatagGCAGATATAGGTCTCTCTATGGGTATATCAGGAACTGAAGTTGCAAAAGAGAGTTCTGACATCATTATTTTGGATGACAATTTTGCTTCAGTAGTAAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                            || || |   | || ||     |  || |||||  |  | ||  |      ||| | | || | ||     ||||| ||  |          | |   ||||| ||||||||||| |||||  ||||||| || || || || |||||||| ||||| |  || || || ||||||||||||||||| || | ||| || |||| |
-----------------------------------------------------------gttcaatac--atttacattcctcgtatgtgtaagctttaaaaata------cactgttattgaggatcacactttctgtgttg---------ccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                            | ||| | |   |   |  |   | ||||  ||   |       || ||| | | | | ||       |  ||||   |  |  ||  |    | |   ||||  ||||||||||||||||  |||||||||||   ||||| || ||||| || ||||| ||||| || |||||||||||||||||||| || ||||| || | |
-----------------------------------------------------------ctcaaata-ggtttctaatatcttttatataaaaaacatttttttatattttccccgctctt----gttcgccttttttttttctttttt--ttttttggactt-tagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG

upper sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 26
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                                                          || |     |  | ||   |  |  |  | |   || | ||  ||  || |      | |  |    ||  ||   || |  || ||  || |  |   |   ||| |||||||||| ||||| || ||||||||||| |||||||||||||| || || || || || || |||||||||||||| || || || ||||| || | |
----------------------------------------------------------ttatggctgtagagtttgga--tgttgtttttccatcttcagcaggttcataatgttgtttctttgtaatgattgatcag--gttgt--atcattttcta---ttgtagGCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCATGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 59

ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCATGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 45

ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCATGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCATGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                              agttaat  putative branch site (score: 248)
                             tagttaat  TA-rich tract