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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagattgattgaagaatttttgtatactatatctatctgaaggtaggatggatttaatttgttgtgggaagggaaggttctgaaatttctgtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT

Basic information

species Glycine max
transcript GLYMA16G13580.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G07110.1 (Arabidopsis thaliana), 3'ss of exon 1
gagattgattgaagaatttttgtatactatatctatctgaaggtaggatggatttaatttgttgtgggaagggaaggttctgaaatttctgtttctgt---agAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT
    |||||       |  ||||| | | | |   | |     |  | | ||   ||| ||           |  |  | ||   ||| ||||| |||   || ||||| ||||||||||| |||||||| |     || || || || |||||||| | ||| ||| ||||| |||||||||||||||| ||||| ||||| 
--ctttgatgtttttgtagttgtacaatgtgtagtttttgttttttgtttgagaaaatgtgccaaatccgatgttgaat-tgttgtttttgtttgtgtggcagTATGATTCCACACAAGACTAAGCGTGGAGCTAATGCACTTGCCCGCTTGAAGGTCTTTGAAGGAGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC

upper sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
gagattgattgaagaatttttgt-atactatatctatctgaaggtaggatggatttaatttgttgtgggaagggaaggtt----ctgaaatttctgtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT
     |  |||   |  ||  || ||      | |   | ||| |    |   | |  ||| ||| |    ||  |  ||     |     || |||   || || ||||| ||||||||||| |||||||| |  || || || ||||| |||||||||| ||||||||| || ||||| || |||||||| ||||||||||||
-----tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattgaatttttggcttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT

upper sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G24830.1 (Arabidopsis thaliana), 3'ss of exon 1
gagattgattgaagaatttttgtatact-atatctatctgaaggtaggatggatttaatt-tgttgtgggaagggaaggttctgaaatttctgtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT
  | |    |   || | |||||  | | || ||| | | | |  |   |   ||| ||  |||  |||           | |||   ||     | |  || ||||| ||||||||||| |||||||| |  || ||||| || ||||||||||| | ||||||| | || ||||| ||||||||| | ||||||||||| 
atggtcagcttttga-tctttgtgcaatgatgtctgtgttagga-attgtatgtttgatagtgtgatggaggatttgaaatgtgatcatttgtcatttacagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCTCTTGCACGTTTGAAGGTGTTTGAGGGAGTACCACCTCCTTATGACAAGGTCAAGAGAATGGTC

upper sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
gagattgattgaagaatttttgtat-actatatctatctgaaggtaggatggatttaatttgttgtgggaagggaaggttctgaaatttctgtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT
 |  ||| |    | |  |||   | |||  ||        |   ||     | ||       |||    |  |||  || |    ||| | ||  ||||| ||||| || |||||||| |||||||| | ||| || || || || ||||||| |||||||||||| ||||| |||||||| ||||| ||||| ||||| 
-attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC

upper sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0029g00020.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------gagattgattgaa--gaatttttgtatactatatctatctgaaggtaggatggatttaatttgttgtgggaagggaaggttctgaaatttctgttt---ctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT
                                        |||    |||  ||| |||| |  | ||| |  || |     |      |||    |||| | || |     ||  | |  |||| ||| | |    ||||| ||||| || |||||||| |||||||| |  || || || ||  | ||||||| ||| ||||| ||||| ||||||||||| ||||| ||||| ||||||
gtgagcttgacttatcattttatatttttctgcattttctattccacgaaacgaagtttttttcattattttcatttatttattaatatgat--gctttgat-tgagccaataaaatcccaaaatctctttctggtttgtagGATGATTCCTCACAAGACTAAGCGTGGAGCCGCAGCGCTTGCCAGATTGAAGGCTTACGAGGGGATTCCACCTCCATATGATAAGATGAAGAGGATGGTT

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|298178143|gb|HO027526.1|HO027526
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|193470062|gb|FK436843.1|FK436843
EST:     CCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|298198649|gb|HO040188.1|HO040188
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|151411210|gb|EV281021.1|EV281021
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|192312241|gb|FK005698.1|FK005698
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|193315341|gb|FK278943.1|FK278943
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|298195471|gb|HO043862.1|HO043862
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|209716349|gb|BW684793.1|BW684793
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|51334831|gb|CO978697.1|CO978697
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|58017414|gb|CX704156.1|CX704156
EST:     CCCATCCACTTCCGCGCACCNTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTCTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|17021875|gb|BM092909.1|BM092909
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|18722168|gb|BM523389.1|BM523389
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|192312242|gb|FK005699.1|FK005699
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|298198972|gb|HO042335.1|HO042335
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|19052887|gb|BM731554.1|BM731554
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
EST: gi|58017241|gb|CX703983.1|CX703983
EST:     CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGG                         AATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA
genomic: CCCATCCACTTCCGCGCACCCTCCAAGATCTTCTGGCGCACCGTTCGTGGgtctgttttt ... gtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatggatttaatttgttgtgggaagggaaggttctgaaatttctgtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT
      atttaat  putative branch site (score: 4)
                                        tttctgtttct  putative PPT
      atttaatttgttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagattgattgaagaatttttgtatactatatctatctgaaggtaggatggatttaatttgttgtgggaagggaaggttctgaaatttctgtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - ctatctg
- - - - - - - - - - - - - - - - - - - - - - -ggatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaagg