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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcagagataatcgaatttgcgatcttttcccttaatcattcaacccaccttatatcccccttaatagtgtgttaatgttgttgggatttgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG

Basic information

species Glycine max
transcript GLYMA03G30110.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
tagcagagataatcgaatttgcgatcttttcc---cttaatcattcaacccaccttatatcccccttaatagtgtgttaatgttgttgggatttgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG
  | |  |||    ||||     || || |      ||      |  |      ||  |     |  | | |  | ||  | |  ||     |    |   ||||||| ||||| ||||||||||| |||||||| ||||| || |||||||||||  | || || ||||| |||||||||||||||||||| ||||| ||||
--gtattgatt-cagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG

upper sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 1
---tagcagagataatcgaatttgcgatcttttcccttaatcattcaacccaccttatatcccccttaatagtgtgttaatgttgttgggatttg--tgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG
   |||||  |   ||   |   || ||    ||||  |    || |   ||  |||| |      ||||     |     |   |||   ||    ||    |||||||||| ||| |||| ||||| ||  |||| || ||||||||||| |||||||| ||  | ||||| ||||||||||| || ||||| ||||| || |
gcatagcactgtgcattataaaggc-atgaaatccc--agcttttgatggcattttat-tgttgaataattccaggc-gccggaattgaatttcaattgccgcagGCTGGTTTCGCCAGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
-----tagcagagataatcg-aatttgcgatcttttcccttaatcattcaacccaccttatatcccccttaatagtgtgttaatgttgttgggatttgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG
     | |||    || |   |||  ||   | ||     ||  |    ||   |   |  |  || ||  | | |||||| |  || | | || |||   |  |||||||||| || ||||| ||||| ||  | || || |||||||||||||| ||||| ||  | ||||| ||||||||||| || ||||| |||||||| |
ctcttttgcatctttatttataatgggcagacattggatgtagac---taatttatgat-caatcctctcgaaactgtgttta-attttggtgaattgaacg-cagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
---tagcagagataatcgaatttgcgatcttttcccttaa-tcattcaacccaccttatatcccccttaatagtgtgttaatgttgttgggatttgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG
   |    |  ||||| |  ||   |||  |     | || | | |  |       |   |||      | |  ||||| |  |||| | || |||   |  |||||||||| || ||||| ||||| ||  | || || |||||||||||||| ||||| ||  | ||||| ||||||||||| || ||||| |||||||| |
caattcatgctataatggcgttcatgataatactattcaagtgacttcagttgtgctg--tccagaacgaaaccgtgttta-attgtggtgaattgaacg-cagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------tagcagagataa-tcgaatttgcgatcttt--tcccttaatcattcaacccaccttatat-------cccccttaatagtgtgttaatgttg---ttggg----atttgtgtgat--agGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG
                                                       || ||        | | |||||| |   |   |    | |||| |||    ||  ||||         || ||  ||| || |  ||   ||   || ||     ||| | ||    |||||||||| |||||||| ||||| ||  |||| || ||||||||||| |||||||| ||  | ||||| ||||||||||| || ||||| ||||| || |
gtatgcatgcttaccgcatatacgactgtaattctcccatgcaaatcgagcatgctaacaatcgcgccttgcatttgctaaggtacattgtctgatcaatcatagtactatatacatatcggtcctctgcataatgcgcaaaatctgaaattaggtctggtttatttggcgcagGCTGGTTTCGCCGGAGACGATGCCCCCCGGGCTGTTTTCCCCAGCATCGTGGGGCGGCCGAGGCACACCGGAGTGATGGTGGGCATGGGACAGAAAGACG

upper sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 1
tagcagagataatcgaatttgcgatcttttcccttaatcattcaacccaccttatatcccccttaatagtgtgttaatgttgttgggatttgtg-tgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG
                                               | |    |  | |  ||  | |||  ||    |    ||| | |||  |   ||||||| ||||||||||| ||||| || ||||| ||||| |||||||||||||| || ||    |||||||| || |||||||| ||||||||||||||||
--------------------------------------------gtgcgctcc-tggcgcggtttcttgtggattttgatccggggggtgtgttcttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

upper sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 1
tagcagagataatcgaatttgcgatcttttcccttaatcattcaacccaccttatatcccccttaatagtgtgttaatgttgttgggatttgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG
                                             | | |||           |  | |  | || ||   |  ||  | | | ||  ||||||| ||||||||||| ||||| || ||||| ||||| |||||||||||||| || ||    |||||||| || |||||||| ||||||||||||||||
------------------------------------------gtgcgctcctggcgcgatttcttgtgg-attttgatccggggggtgtgtttttg-cagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

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|209701261|gb|BW652268.1|BW652268
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatatcaat ... tgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
EST: gi|193601495|gb|FK552116.1|FK552116
EST:     ATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
genomic: ATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatatcaat ... tgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
EST: gi|193642633|gb|FK593331.1|FK593331
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatatcaat ... tgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
EST: gi|208103976|gb|GD902651.1|GD902651
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatatcaat ... tgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
EST: gi|298181218|gb|HO022657.1|HO022657
EST:     CCGAGGATATTCAACCGCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatatcaat ... tgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
EST: gi|208197124|gb|GD999339.1|GD999339
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatatcaat ... tgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
EST: gi|120530859|gb|EH258992.1|EH258992
EST:     GCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
genomic: GCGATAATGGAACCGGAATGGTCAAGgtatatcaat ... tgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
EST: gi|254315473|gb|GR825282.1|GR825282
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatatcaat ... tgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTG
EST: gi|16346204|gb|BI971799.1|BI971799
EST:     CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCANTT-T
genomic: CCGAGGATATTCAACCCCTCGTTTGCGATAATGGAACCGGAATGGTCAAGgtatatcaat ... tgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCA-TTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccaccttatatcccccttaatagtgtgttaatgttgttgggatttgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG
                          tgttaat  putative branch site (score: 3)
                 ttaatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcagagataatcgaatttgcgatcttttcccttaatcattcaacccaccttatatcccccttaatagtgtgttaatgttgttgggatttgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - cccttaa
- - - - - - - - - - - - - - - - - - - - -tcaaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggg