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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA

Basic information

species Glycine max
transcript GLYMA10G16090.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G132144_T01 (Zea mays), 3'ss of exon 6
gttgttcttgtttgtcagttggtctttggagtagatgcatgttctt-gtttgttgtgcttaaaatatt--taatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
   |||||   ||  || |  || ||       | | ||||||||| |||  |||||   |  ||||    ||    |     |  ||| |||||   ||||| ||  |||||||| |||| ||| | || | ||| ||||||||||||||||||  |||||||||||| ||||| ||||| ||||| ||||     || |
---gttctaactt--caat--gtttt-------gttccatgttctttgttctttgtgtacactatatcaccaaccatgttccttcctgatctttgg-acagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 2
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
           || | | ||     ||    |   ||    || || ||||| || |   | ||    ||    |     |  ||| |||||  |||||| ||  |||||||| |||| ||| | || | ||| ||||||||||||||||||  |||||||||||| ||||| ||||| ||||| ||||     || |
----------gttctaacttcaatgttttgttctgtgttctttgttctttgt-gtacactatatcaccaaccatgttccttcctgatctttgg-gcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G119381_T01 (Zea mays), 3'ss of exon 1
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
   |||||   ||    |||    ||||       ||    || || ||||| || |   | ||    ||    |     |  ||| |||||  |||||| ||  |||||||| |||| ||| | || | ||| ||||||||||||||||||  |||||||||||| ||||| ||||| ||||| ||||     || |
---gttctaacttcaatgttttgttttg-------tgttctttgttctttgt-gtacactatatcaccaaccatgttacttcctgatctttgg-gcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G038313_T01 (Zea mays), 3'ss of exon 2
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatt--taatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
         |||   |  |   | ||| |  ||| ||  | |  ||| |  ||||   |   |||||  |||  | |     |  | | |||| | |||||| ||  |||||||| |||| ||| | || | ||| ||||||||||||||||||  |||||||||||| ||||| ||||| ||||| ||||     || |
---------gttctaccatcaatgtttcg--tag-tgtgt-tctttgctctttgtatatgttatattagtaaccttgttccttccttatcttt-tggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G159061_T01 (Zea mays), 3'ss of exon 1
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
           || | | ||     ||    |   ||    || || ||||| || |   | ||    ||    |     |  ||| |||||  |||||| ||  |||||||| |||| ||| |  | | ||| ||||||||||||||||||  |||||||||||| ||||| ||||| ||||| ||||     || |
----------gttctaacttcaatgttttgttctgtgttctttgttctttgt-gtacactatatcaccaaccatgttccttcctgatctttgg-gcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G076337_T01 (Zea mays), 3'ss of exon 3
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
   |||||     |   |  |  |||||   |   ||    || || ||||| || |   | ||    ||    |     |  ||| |||||  |||||| ||  |||||||| |||| ||| |  | | ||| ||||||||||||||||||  |||||||||||| ||||| ||||| ||||| ||||     || |
---gttctaaccgg---gacgtgctttgttctg--tgttctttgttctttgt-gtacactatatcaccaaccatgttccttcctgatctttgg-gcagAACTTCTCATCACCTCTGAATCAGCTCTAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATGAAAATGGTAGAAATGGGATCA

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G105461_T01 (Zea mays), 3'ss of exon 3
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
   |||||   ||    |||    ||||       ||    || || ||||| || |   | ||    ||    |     |  |||  ||||  |||||| ||  |||||||| |||| ||| | || | ||| ||||||||||||||||||  |||||||||||| ||||| |||  ||                  
---gttctaacttcaatgttttgttttg-------tgttctttgttctttgt-gtacactatatcaccaaccatgttccttcctgatatttgg-gcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATATCAG-----------------

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G038028_T01 (Zea mays), 3'ss of exon 7
gttgttcttgtttgtcagttggtctttggagtagatgcat-gttct-tgtttgttgtgcttaaaatatt--taatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
                        | |    |  |||  | ||||| ||||  |||||   |  ||||    ||    |     |  ||| |||||  |||||| ||  |||||||| |||| ||| | || | ||| ||||||||||||||||||  |||||||||||| ||||| |||  ||                  
----------------------gttctaacttcaatgttttgttctgtgttctttgtgtacactatatcaccaaccacgttccttcctgatctttgg-gcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATATCAG-----------------

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G094083_T03 (Zea mays), 3'ss of exon 9
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
           || | | ||     ||    |   ||    || || ||||| || |   | ||    |||   |     |  ||| |||||  | |||| ||  |||||||| |||| ||| | || |  || ||||||||||||||||||  |||||||||||| ||||| |||  ||                  
----------gttctaacttcaatgttttgttctgtgttctttgttctttgt-gtacactatatcaccaatcatgttccttcctgatctttgg-gtagAACTTCTCATCACCTCTGAATCAGCTCCAGAATAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATATCAG-----------------

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G107893_T01 (Zea mays), 3'ss of exon 5
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
   |||||   ||    |||    ||||       ||    || || ||||| || |   | ||    ||   |   |  |     |  ||   |||||| ||  |||||||| |||| ||| | || |  || ||||||||||||||||||  |||||||||||| ||||| |||  ||                  
---gttctaacttcaatgttttgttttg-------tgttctttgttctttgt-gtacactatatcaccaacccatgttccttcctgatatttgggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAATAGGATATGGCTGATGCATTGGGCTCTGTTCATCTTCTTTAACCATATCAG-----------------

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 3'ss of exon 3
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatattta-------atatagactggtggtgaact-ttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
                 ||| || |||  |     | |  |||   |    |||   | || |||  |        |||||  ||       |  | || || |||| |||| |||| || || ||||||||||| | ||| || ||| ||||||||||| ||||||  ||||||||||| ||||| ||||| || ||||| || |
-----------------gttagtatttaaaacttcttctagtttgcgacctttgaaatcaatatagatgtgagagtatatatgctaactaccatttgttttttcagAGTTTTTCATCGCCGTTAAACCAGGTGCAGAACAGGATTTGGTTGATGCATTGGGGTCTGTATATCTTTTTTAACCATGATAATGGAAGGACACAGATCA

upper sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 3
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
||   | |  | ||    |||||   |        || |   | |  ||||||  || | | ||||||        ||  |  |||  | | ||||||| ||  || |||||| |||| ||||||||||| ||||||||||| |||||||||||||| ||||||||||| || |||||||||||| ||||||| ||||
gtcactgtcatatgcatattggttgctc-------tgtacagtttgttttgtt--gcatgatatatttg-------ctaatcatgagttctcttgcagAGTTACGCTTCACCTCTGAATCAGGTGCAAAGTAGAATATGGCTAATGCATTGGAGTCTCTTCATCTTTTTCAACCATGACAATGGGCGAACACACATAA

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|7147523|gb|AW509445.1|AW509445
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|193447481|gb|FK415006.1|FK415006
EST:     ACATTGCTCTTGAAGAGCTCAATCGCTTGAAGGAAATCATTGATTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|19053227|gb|BM731894.1|BM731894
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|13789066|gb|BG651657.1|BG651657
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|254316955|gb|GR828492.1|GR828492
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAG-TGCAAAGCAGAA-ATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|193323769|gb|FK291293.1|FK291293
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCAATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCA
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCA-TCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCA
EST: gi|193588990|gb|FK541816.1|FK541816
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|209707121|gb|BW661575.1|BW661575
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|21479769|gb|BQ576452.1|BQ576452
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|7588257|gb|AW704056.1|AW704056
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|16105694|gb|BI893434.1|BI893434
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|10709957|gb|BF009681.1|BF009681
EST:     ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: ACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
EST: gi|21888755|gb|BQ741968.1|BQ741968
EST:     GCTTGAAGGAAATCATTGACTCAAAG                         AATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT
genomic: GCTTGAAGGAAATCATTGACTCAAAGgttgttcttg ... tttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA
                     atttaat  putative branch site (score: 4)
                                            ctttgtt  putative PPT
        ttgtgcttaaaatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcagAATTTTGCATCACCTTTGAACCAGGTGCAAAGCAGAATATGGCTGATGCATTGGAGTCTGTTCATCTTTTTTAATCATGACAATGGGAGAACACAAATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA