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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttggctcttctctttgtttattcctgtctcatttcatcacatgttactataaagcaaaatagaatgatgaaacctttcatgacatgttttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCT

Basic information

species Glycine max
transcript GLYMA09G31940.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G31940.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G68660.1 (Arabidopsis thaliana), 3'ss of exon 2
ttgttggctcttctctttgtttattcctgtctcatttcatcacatgttactataaagcaaaatagaatgatgaaacctt-tcatgacatgttttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCT
           | |  |||  ||   |  ||| | ||   |   | | | ||| |  |||| |   ||| | |    |  | ||    || |||    |||||||||   ||| | | | ||||||||| | ||  | || ||||||||||||||||||||| | |||||||| || || |||||||||||||| ||||| 
----------gtattattgcctacaacaatctgaattttcc---tttcaatatgat-caaattcatatgcttatttgtgattatactttgctttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAACTTCAACAAGAGGGAATATGTGGTTCAGGTGTTGATGAAGGTAATACCC

upper sequence: GLYMA09G31940.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G68660.2 (Arabidopsis thaliana), 3'ss of exon 2
ttgttggctcttctctttgtttattcctgtctcatttcatcacatgttactataaagcaaaatagaatgatgaaacctt-tcatgacatgttttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCT
           | |  |||  ||   |  ||| | ||   |   | | | ||| |  |||| |   ||| | |    |  | ||    || |||    |||||||||   ||| | | | ||||||||| | ||  | || ||||||||||||||||||||| | |||||||| || || ||||||||||||         
----------gtattattgcctacaacaatctgaattttcc---tttcaatatgat-caaattcatatgcttatttgtgattatactttgctttgattcagGAAATCAAAGAAGATAGCTCCACCTTACAGGGTGATACTACACAATGACAACTTCAACAAGAGGGAATATGTGGTTCAGGTGTTGATGAAG---------

upper sequence: GLYMA09G31940.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g04020.t01 (Vitis vinifera), 3'ss of exon 2
ttgttggctcttctctttgtttattcctgtct--catttcatcacatgttact-ataaagcaaaatagaatgatgaaacctttcatgacatgttttctgc-----cagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCT
       |||||||| | |  | ||| | |||  |||    |   | || ||| || || |  |||   |  |  | |  |  |   |    || | ||      |||||||||  ||||||  ||||||||||| |||||  ||||||| || ||||||| ||| |||||||| |||||||| |||||| |||||||||| || |||
-------ctcttctcatggaat-ttcatatctatcatgaattggaaggtgactgatgaaacttaattagaacacaagatttcactaaattgattgtttggatttgcagGAAATCAAGGAAAATGTCCCCACCTTATCGAGTACTGCTGCATAACGACAACTACAATAAGCGAGAGTATGTTGTTCAAGTGCTGATGAAGGTTATCCCT

upper sequence: GLYMA09G31940.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S40_52V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------ttgttggctcttctctttgtttattcctgtctcatttcatcacatgttactataaagcaaa-------atagaatgatgaaacctttcatgacatgttttc---tgcca--gGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCT
                                                   |     ||   | |   ||  | ||     |   ||||| ||  |     |  |     ||        | | ||  |   |  |||  || | ||| |||   | |||  ||||   |  |||||  || || || || || ||  |||| ||||| ||||||||||| ||||| ||||||||||| |||||  || ||||||  || || 
gtgggtccttcactgctcttcctatgtcttggttcaatcaagtcttacatgtgaagagcgtctattcatgcctcttatcaacatgtttcagcatttacatttgcagtttcaattttcaggtggcattttctgaatttttctggc-tgtcttcgtgtaccatagGAAGAAGAAGAAAATGTCACCTCCATATCGTGTCATGCTCCACAACGACAACTTCAATAAGCGTGAATATGTTGTCCAAGTTCTGCTGAAGGCTATCCCC

upper sequence: GLYMA09G31940.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S32_331V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------ttgttggctcttctctttgtttattcctgtctcatttcatcacatgttac-tataaagcaaaatagaatgatgaaacctttcatgacatgttttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCT
                                                       |  | ||||    |||   |  | | || |       | |  |   |  |   |  |   ||    || | |  ||| ||    | |  ||     ||||||      ||| |  || || || || || ||| |||| ||||||||||||||||||||||| ||||| ||||| |||||  ||||||| |  || || 
gtgagtttaccatttctctttcaatacttcactagttcatttcgatgctgcatgcgaagactctcaattttacctggtacagtatgtgcatgttaggttcaatatcccagtcggcatgtcgtggttattcctctctactcttacttgaatgcagGAAGAAAAAGAAGATGTCACCCCCATATCGTGTTATGCTCCACAATGACAACTTCAACAAGCGTGAATACGTTGTCCAAGTTCTGATGAAAGCCATTCCC

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|120491374|gb|EH219541.1|EH219541
EST:     CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAG                         GAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
genomic: CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAGgtaaccaacg ... tttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
EST: gi|10254894|gb|BE822660.1|BE822660
EST:     ATAGAGACAACATCACNNGGTCGGGNATCTGAATTTGACTTAAG                         GAAATCGCGGAAAACATCCCCACCNTACCGAGTTTTGCTGCACAATGACAA
genomic: ATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAGgtaaccaacg ... tttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
EST: gi|209699630|gb|BW655722.1|BW655722
EST:     CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAG                         GAAATCGCAAAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
genomic: CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAGgtaaccaacg ... tttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
EST: gi|11413447|gb|BF425458.1|BF425458
EST:     CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAG                         GAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
genomic: CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAGgtaaccaacg ... tttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
EST: gi|209716301|gb|BW657604.1|BW657604
EST:     CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAG                         GAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
genomic: CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAGgtaaccaacg ... tttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
EST: gi|298166564|gb|HO010003.1|HO010003
EST:     CCAACCATAGAGACGACATCACCTGGTCGGGAATCTGAATTTGACTTAAG                         GAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
genomic: CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAGgtaaccaacg ... tttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
EST: gi|209718755|gb|BW671956.1|BW671956
EST:     CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAG                         GAAATCGCAAAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA
genomic: CCAACCATAGAGACAACATCACCTGGTCGGGAATCTGAATTTGACTTAAGgtaaccaacg ... tttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttactataaagcaaaatagaatgatgaaacctttcatgacatgttttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCT
                                            ttttctgcc  CT-rich tract
     tataaagcaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttggctcttctctttgtttattcctgtctcatttcatcacatgttactataaagcaaaatagaatgatgaaacctttcatgacatgttttctgccagGAAATCGCGGAAAACATCCCCACCTTACCGAGTTTTGCTGCACAATGACAACTTCAACAAGCGAGAATATGTTGTGCAAGTGTTGATGAAGGTGATACCT

-tgttggc
- - - - - - - - - - - - - ctgtctc
- - - - - - - - - - - - - - - - - - - - cacatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - aagcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacatgt