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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG

Basic information

species Glycine max
transcript GLYMA13G40960.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 7
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
                      |  || |||    ||||    |||   | | |   |||  |  || |  ||  | |||||         || ||| |     || ||    |||| || || ||||| || || || ||||| ||||||||  | ||||| ||||||||||||||||||||||| |||||||||||||| ||  | ||
---------------------gtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagtt-ctccttaata------agtattt-tccaatctatctctgtagAGATCCGAATTGCCAGGATTTTCAACACCTATGGACCTAGGATGAACATTGATGATGGGCGTGTTGTTAGTAACTTCATTGCTCAGGCCGTACG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 8
gtaatttcttgtcttc--ttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
|||||   |  ||||    ||    |||||| |   |||||     |      | |    ||    | ||   || |   ||  |  |  |   | |||||      | ||    ||||||| || ||||| || || || ||||| ||||||||| | ||||| ||||| ||||| |||||||||||||||||||||||||| ||  | ||
gtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataac--tctaggcttatgatttgtcctca-gcaatatttataatctatgtc--tgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 8
gtaatttcttgtctt---cttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
||||    |  ||||   |||   |||  |  ||  |  |   | |    |     |     | |  | |    || |   ||   || |   ||| |||||      | ||    ||||||| || ||||| || || |||||||| ||||| ||  | ||||| ||||||||||| |||||||||||||||||||||||||| ||  | ||
gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttaacggtatttatcatctatgtc--tgtagAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 9
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtt-tacacatatccagta-gagatttatctttgtttcttaactccttgtggt--gtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACC-ACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
    |  |   || |||||  |||  | ||   | | | |   |  ||  | | |    || | |||   |||  | || | |  |  || | |   || | | ||  || |     ||||||| || ||||| || || |||||||| ||||| || | | ||||| ||||||||||| |||||||||||||||||||||||||| ||  | ||
---gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttgacagtatttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTTAACACCTATGGGCCTAAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 4
gtaatttcttgtcttcttttccttgtaatttctt-ctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
       |||    |    |  | |||  |  |  | |  ||||||   | ||| |     | | ||    ||| |||||||||    | |    | |||||||          ||||||| || ||||| || || || ||||| ||||| ||  | ||||| ||||||||||| |||||||||||||||||||||||||| ||  | ||
------acttaaacttcaatattagtagctcatagccctctttgttatgagataact--ctgggcttatgatttttttcttaacagtatttatcatctatgtct---------gtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 5
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtt-tacacatatccagta-gagatttatctttgtttcttaactccttgtggt--gtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
    |  |   || |||||  |||  | ||   | | | |   |  ||  | | |    || |||||   |||  | || | |  |  || |     || | | ||  || |     ||||||| || ||||| || || || ||||| ||||| ||  | ||||| ||||||||||| |||||||||||||||||||||||||| ||  | ||
---gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgagataactctgggcttatgatttttttcttaacagtatttatcatctatgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGTCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 14
gtaatttcttgtcttctttt----ccttgtaatttctt-ctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
||||    |  ||||    |    | |    |||  |  |||||  |  |      |||    ||    |     | || || ||   || |    ||||||||      | ||    ||||||| || ||||| || || || ||||| ||||| ||  | ||||| ||||||||||| |||||||||||||||||||||||||| ||  | ||
gtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgatttttt-ttcttaacagtgtttatcatctatgtc--tgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 7
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtt-tacacatatccagtagagatttatctttgtttcttaactccttgtggt--gtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
    |  |   || |||||  |||  | ||   | | | |   |  ||  | | |    ||     | |   | |  |  | | |  || |     || | | ||  || |     ||||||| || ||||| || || || ||||| ||||| ||  | ||||| ||||||||||| |||||||||||||||||||||||||| ||  | ||
---gtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtagAAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
                       |  ||||  |     ||||         |    |     ||||||   || ||   | | |  || |    | ||| | ||    ||   |||| |||||||| || || || || ||||||||||| || || ||||| ||||||||||| || ||||| ||||||||||||||||| || ||  |
----------------------gtaaaattaatcactcttttaccattttcttgaaaactttgatttaagcttattggctgattagttattacttctat-tgtctggccattgtagAGATACGCATAGCGAGGATATTCAACACATATGGTCCTCGTATGAACATTGATGATGGTCGCGTTGTGAGCAACTTCATTGCTCAGGCTCTCAG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtt--tcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
        |    | | ||| ||     | ||   |||  || | | |   ||    | |   |  |||  |  ||   ||| | |||||    ||||| ||| || | |     ||||||| |||||||| |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||| |||||||||||||| |||||||| ||
-------gtaagttgcattttctcaggctctcgcttcaactt-tctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctt--tgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCGATGATGGCCGTGTTGTAAGCAACTTCATTGCACAAGCACTCCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
          || ||||  | |   |||  ||    |||    |||     ||||||||   ||||  | |  | |||| |     |||   ||||| |    | |||     ||||||| |||||||| |||||||| ||||||||||| || || ||||| || ||||||||||||||||| ||||||||||||||||||||||| ||
------gtcagttttctacttccc-taaactcactgcatcacttttttctttatccagt---gattcctttaagattctca-----ttggcctgtttgt----cattt----gtagAAATCCGCATTGCTAGAATCTTCAACACATATGGTCCTCGAATGAACATCGATGATGGGCGTGTTGTGAGCAACTTCATTGCTCAAGCACTCCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 8
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
              |   ||   |||  ||| || | ||  ||   | ||   | || |  | ||  |  |||  |   ||        || ||||| | | |  |||  ||  ||||||||||||||| ||||| || ||||||||||| || |||||||||||||||||||| |||||||| ||||| ||||| ||||||||||||||
-------------gtaacttttgtgtttttttttttaatcctgaacaaac---ttcaatgaatatgaagttttaatatgta--------tgttgtttctttatattttggac--agAAATACGCATTGCTAGAATTTTCAACACATATGGGCCCCGCATGAATATTGATGATGGACGTGTTGTCAGCAATTTCATAGCTCAAGCACTTCG

upper sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
          |  | |  |    ||||  |     |    | |  |      || |     || ||     ||| |  | | |||       || || ||       |      |||||| ||  | ||| |||| |||||||| ||||| || ||||||||||| || |||||||| || || ||||| || |||||||||||| |  |
--------aaggatgcgatgaaatgtagctctgagtgtagtagcatcactgaattccaagaagcttggatcttggtcataatctc-------tgctt-tgctattcgtggtggcagAAATCCGTGTAGCACGAATTTTTAACACCTATGGGCCTCGCATGAATATCGACGATGGGCGAGTAGTCAGCAATTTTATTGCTCAAGCATTAAG

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|151406393|gb|EV276208.1|EV276208
EST:     ACGGGTGGCCGAGACATTGATGTTTGATTACCATAGGCAGCATGGGATTG                         AAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTG
genomic: ACGGGTGGCCGAGACATTGATGTTTGATTACCATAGGCAGCATGGGATTGgtaatttctt ... ttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTG
EST: gi|151404362|gb|EV274172.1|EV274172
EST:     ACGGGTGGCCGAGACATTGATGTTTGATTACCATAGGCAGCATGGGATTG                         AAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTG
genomic: ACGGGTGGCCGAGACATTGATGTTTGATTACCATAGGCAGCATGGGATTGgtaatttctt ... ttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTG
EST: gi|19052776|gb|BM731443.1|BM731443
EST:     ACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG                         AAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTG
genomic: ACGGGTGGCCGAGACATTGATGTTTGATTACCATAGGCAGCATGGGATTGgtaatttctt ... ttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatagAAATACGCATTGCAAGAATCTTTAACACATATGGACCACGCATGAATATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAAGCACTTCG
               tcttaac  putative branch site (score: 2)
                                 tttatgtctcctttc  putative PPT
             tttcttaa  TA-rich tract