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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_T04
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

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|67041185|gb|CO467440.1|CO467440
EST:     TGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCATCTTTGCACGCAG                         GCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGA
genomic: TGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATG-AGgtttgtggac ... aaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG
                              agttaat  putative branch site (score: 4)
                             tagttaat  TA-rich tract