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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttggggctaatgtgtttatggttgacattatgaacttgtaatgaagattactggtgttgttgtggaaagttttctaagacggatgtttgtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT

Basic information

species Glycine max
transcript GLYMA08G46860.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46860.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
atttggggctaatgtgtttatg-gttgacattatgaacttgtaatgaagattactggtgttgttgtggaaagttttctaagacggatgtttgtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT
  || | |   ||    | |||    |   | || ||  || | |     ||  |  |   ||| |||  |  ||   |     |   |||||| |||||||||||| ||||||||||| ||||| || |  ||||| ||||| || |||||||| | |||||| || || |||||||| |||||||  ||||| ||||||
tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattga-atttttggcttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT

upper sequence: GLYMA08G46860.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G24830.1 (Arabidopsis thaliana), 3'ss of exon 1
atttggggctaatgtgtttatggttgacattatgaacttgtaatgaagattactggtgttgttgtg--gaaagttttctaagacggatgtttgt-gtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT
||     |||  ||  | | ||  ||  || |||    ||| | |||   ||    || |  ||||  | | | |||  ||   |    |||||  ||| ||||||||| ||||||||||| ||||| || |  ||||||||||| || |||||||||| ||||||  | || |||||||||||||||  |||||| ||||| 
atggtcagcttttg-atctttg--tgcaatgatgtctgtgttaggaattgtatgtttgatagtgtgatggaggatttgaaatgtgatcatttgtcatttacagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCTCTTGCACGTTTGAAGGTGTTTGAGGGAGTACCACCTCCTTATGACAAGGTCAAGAGAATGGTC

upper sequence: GLYMA08G46860.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
-atttggggctaatgtgtttatggttgacattatgaacttgta-atgaagattactggtgttgttgtggaaagttttctaagacggatgtttgtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT
  ||||| ||   |||   | |  || || | || |  |   | |   || ||| |        |||    | |    |     || | | | |  ||| |||||||| || |||||||| ||||| || | ||| || ||||| ||||||||||  |||||||| || ||||| || ||||| ||||  ||||||||||| 
attttggtgcc--tgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC

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|9986841|gb|BE660949.1|BE660949
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGAGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|298195955|gb|HO044346.1|HO044346
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGAGGGGAAGCTGCTCTCGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|193730000|gb|FK667844.1|FK667844
EST:     CCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|193544119|gb|FK502598.1|FK502598
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGACGACGGGGAAAGACTGCTCTTGCGCGAT
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAG-CG-CGGGGAA-G-CTGCTCTTGCGCGAT
EST: gi|298189729|gb|HO038132.1|HO038132
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGAGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|298189786|gb|HO038189.1|HO038189
EST:     CCCATACATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGAGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|192325948|gb|FK016625.1|FK016625
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|193380148|gb|FK347854.1|FK347854
EST:     ATCCTATTTTCCGTTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: ATCC-A-TTTCCG-TGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|18717939|gb|BM523010.1|BM523010
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|193428398|gb|FK394018.1|FK394018
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGC-GGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|14011338|gb|BG726260.1|BG726260
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|15286024|gb|BI469915.1|BI469915
EST:     GGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: GGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|208043863|gb|GD842345.1|GD842345
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|208183181|gb|GD982789.1|GD982789
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACTAAAGTCGTCGGGGAAGCTGCTCTTGCGCGATT
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGAC-AAAG-CG-CGGGGAAGCTGCTCTTGCGCGATT
EST: gi|193414001|gb|FK376595.1|FK376595
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGC-GGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|105633518|gb|DW246881.1|DW246881
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGAGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|163920729|gb|EH039986.1|EH039986
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGAGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|151407543|gb|EV277358.1|EV277358
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|193321509|gb|FK284049.1|FK284049
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGG-AAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
EST: gi|4297327|gb|AI442602.1|AI442602
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTT
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagtactg ... gtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagattactggtgttgttgtggaaagttttctaagacggatgtttgtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT
                      aaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttggggctaatgtgtttatggttgacattatgaacttgtaatgaagattactggtgttgttgtggaaagttttctaagacggatgtttgtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - -gctaatg
- - - - - - - - - - - - - - - tatgaac
- - - - - - - - - - - - - - - - - - - - -aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgtt