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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttgacatggatgacctttgatggaaatataattgtgaagcttttaaagttgtgggatcttcattacctgaatttgttgtttcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG

Basic information

species Glycine max
transcript GLYMA10G43990.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 1
aggttgacatggatgacctttgatgga---aatataattgtgaagcttttaaagttgtgggatcttcattacctgaatttgttgtttcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG
|  ||  |  |  ||| |  ||| |     |||||  |||       ||| || |  |  | || ||    | ||   |   | |  | |  |        ||||  | ||| | ||| ||||| | |||||||||||||  ||||| || ||||| |||||||| ||||| |  ||||||||||| ||||| |
aaatt--ctggagtgatcggtgaagtgtttaatatggttgacttcagtttcaactgatttgttcatcga-gcttgctgtaactatggccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 1
aggttgacatggatgacctttgatggaaatataattgtgaagcttttaaagttgtgggatcttcattacctgaatttgttgtt-tcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG
    |     |  | |         | |         ||    |  |||   | |   || ||   |  ||| ||||||| |    | ||||      |||||  | ||| | ||| | ||| | ||||||||||||||||| || || || ||||||||||||||||| |  ||||||||||| ||||| |
-aactattgagcgtaattcacctcagcagagctgccatgtgtttgataagcatctcttatgttatgtgactggatttgttctaactgtggttggtatgtagGAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 1
aggttgacatggatgacctttgatggaaatataattgtgaagcttttaaagttgtgggatctt-cattacctgaatttgttgtttcggggttacatgat--agGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG
   ||  ||   ||      | ||    || | | | |    | |||   || | | |||||| |  | | |  | || |  |  |   |||   ||    ||    | || || ||    |||||||||||| |||||||||||||||| || || || || ||||| || | ||| |||||||| |||||||
-tctttccaatcatttatgctcatttctatgtgactattcctcctttt--gtcgggtgatctttctctgcttataattttgataaccatgtttactggcgcagATGGACGATCTGAAAACTTTCCGACAATGGAGAAGCAGAACTCCTGGTCACCCAGAAAATTTTGAAACACCTGGCGTTGAAGTCACCACAG

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------------------------------------------------------------------aggttgacatggatgacctttgatggaaatataattgtgaagct----tttaaagttgtgggatc--ttcattacctgaatttgttgtttcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG
                                                                            || |||    |  |  |   | ||      ||  |||      |    |||| | |||| | | |   | |  |  ||     |  || | |  |||   |  |||||  ||||  | |||   ||||| ||||||||||| |  ||||| |||||||||||||| |||||||| | ||| |||||||  || || |
gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagatttagaattgtagaaccaacttaagatttgctgaagcagtgttgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 1
aggttgacatggatgacctttgatggaa-atataattgtgaagcttttaaagttgtgggatcttcatta----cctgaatttgttgtttcggggttacatgat-agGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG
        | ||||      ||||| || | ||   | ||   |||   |   | |   || || |||     | ||| ||     | | ||  ||   || | ||||| | ||  | |||   ||||||||||||||||| ||||||||||| || || |||||||| ||||| | ||| ||||||||||| || |
------ttaaggatatatgctgatgaaagaaatccatatgtttcttcagattatatcacattttaattttgttcatgacttccccctctgggatttgattgctcagGAAGAGGATTTGAAGTCTTTCCGACAATGGGGAAGTAGAACTCCTGGTCACCCAGAGAACTTCGAGACACCTGGGGTTGAAGTGACAACTG

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ07676 (Selaginella moellendorffii), 3'ss of exon 1
aggttgacatggatgacctttgatggaaatataattgtgaagcttttaaagttgtgggatcttcattacctgaatttgttgtttcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG
           |  | |  |  || ||  | || ||  ||   |||  |          || |    || || |||| ||| ||    ||| |     ||||| | ||  | ||| ||||||| |||||||| |||||||||||||| ||||| |||||||| ||||| |  || || ||||| || || |
-----------gtaggctctccattga--tctagtttcgagcttttctatcaaagttcttcctttcaacatggatttcttgctt----gtttc----cagGAAGAGGATTTGAAGCAATTCCGTCAATGGGGCAGCAGAACTCCTGGCCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTG

upper sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ07729 (Selaginella moellendorffii), 3'ss of exon 1
aggttgacatggatgacctttgatggaaatataattgtgaagcttttaaagttgtgggatcttcattacctgaatttgttgtttcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG
           |  | |  |  || ||  | || ||  ||   |||  |          || |    || || |||| ||||||    ||| |     ||||| | ||  | ||| ||||||| |||||| | |||||||||||||| ||||| |||||||| ||||| |  || || ||||| || || |
-----------gtaggctctccattga--tctagtttcgagcttttctatcaaagttcttcctttcaacatggatttcttgttt----gtttc----cagGAAGAGGATTTGAAGCAATTCCGTCAATGGAGCAGCAGAACTCCTGGTCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTG

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|213618089|gb|DB963722.1|DB963722
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACNATGGGGAAGCAGAACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
EST: gi|8825831|gb|BE209561.1|BE209561
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
EST: gi|209703817|gb|BW656895.1|BW656895
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
EST: gi|209701314|gb|BW655909.1|BW655909
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
EST: gi|213602270|gb|DB958530.1|DB958530
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCG
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCG
EST: gi|209724875|gb|BW669564.1|BW669564
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCC
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCC
EST: gi|209698042|gb|BW675661.1|BW675661
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGA
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGA
EST: gi|213611583|gb|DB960863.1|DB960863
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAG
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAG
EST: gi|209715669|gb|BW674355.1|BW674355
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
EST: gi|213591657|gb|DB969757.1|DB969757
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACAATGGGGA
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGA
EST: gi|209704746|gb|BW656700.1|BW656700
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
EST: gi|209700040|gb|BW652940.1|BW652940
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
EST: gi|18692759|gb|BM521607.1|BM521607
EST:     GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAG                         GAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT
genomic: GCATGCTCCAATATGCTCTCCTTCACCTTGCTGGCTATGACACTGTTCAGgtcagttttt ... tacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaagttgtgggatcttcattacctgaatttgttgtttcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG
                           aatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttgacatggatgacctttgatggaaatataattgtgaagcttttaaagttgtgggatcttcattacctgaatttgttgtttcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - -catggat
- - - - - - - -acctttg
- - - - - - - - - - - - - aaatataa
- - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt