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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtctgactaggagtaggagttcacttttgttatccatgtgacatagactttctgttagcaaggacgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATT

Basic information

species Glycine max
transcript GLYMA07G07270.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G07270.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 1
ggtctgactaggagtaggagttcacttttgttatccatgtgacatagactttctgttagcaaggacgtgagga----acactattaattttttgtttccttc----agCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATT
        | || | |   | ||||    |      |  ||  || |  |  ||| | |    || ||||  |      | || ||||||| | ||||||      ||||| ||||| ||  | ||||  || |||||||||||||| |||||||||||||||||||| || |||   || ||||||||  ||||  |  ||||||| 
-------gtgggggaaatgggtcacggcggcc-caaaaatgttatggtttgactgcttgagtagatgtgattatattgtagtagtaattttgtttttcctatttgtagCGCGGCTGTTAACTCGGAGAACGGCGAGGAAGTTGCCATCAAGAAGATTGGCAATGCATTCGACAACCATATCGATGCCAAGCGGACACTGAGAGAAATC

upper sequence: GLYMA07G07270.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G01560.1 (Arabidopsis thaliana), 3'ss of exon 1
ggtctgactaggagtaggag-ttcact-tttgttatccatgtgacatagactttctgttagcaaggacgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATT
  |  |    |   | | |  ||  ||  || |     |  |||   |||  |  |  | |  |  |   |      |  || | || ||| | |  || || |||||    ||| | ||||| ||||||||||| || || ||||||||||| ||||||||||  ||||  || || || || || || ||  |||| |||
--ttcggtgggtttttgtaactttgctacttatctcatagttgattaagagatcattgtggtgaatagaagttttgaaggatcatttatttatctgatttagTGCTGCATGGAATTCGGAGACGGGTGAGGAAGTAGCGATCAAGAAGATTGGTAATGCATTTGGCAACATTATCGACGCTAAGAGAACTTTGAGAGAGATT

upper sequence: GLYMA07G07270.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
ggtctgactaggagtaggagttcacttttgttatccatgtgacatagactttctgtt--agcaaggacgtgaggaacactattaattttttg--tttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATT
            | ||| || |      | | ||| |  |||| |    | ||||||  | |||  | |||| | | ||   |  ||||||   ||||||||||||||||  | ||  |||||||| | |||||||||||||||||||||||||| |||||||||||||| || |||||||||||| |||| ||||| ||||||
----aagggcacaatagaagctacacaatttcatctaattgacttcatttctctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT

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|11275203|gb|BF325526.1|BF325526
EST:     TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTG                         CGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTGgtaagtcaaa ... tttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|151396148|gb|EV266025.1|EV266025
EST:     TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTG                         CGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTGgtaagtcaaa ... tttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|254328119|gb|GR835084.1|GR835084
EST:     TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTG                         CGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTGgtaagtcaaa ... tttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|22522756|gb|BU081567.1|BU081567
EST:     TATGTCCCTCCTATTCGTCCTGTGGGTAGAGGCGCTTATGGTATTGTTTG                         CGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTGgtaagtcaaa ... tttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|254315198|gb|GR830191.1|GR830191
EST:     TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTG                         CGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTGgtaagtcaaa ... tttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|9264552|gb|BE352699.1|BE352699
EST:     TATGTCCCTCCTATTCGTCCTGTGGGTAGAGGCGCTTATGGTATTGTTTG                         CGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TATGTCCCTCCTATTCGCCCTGTGGGTAGAGGCGCTTATGGTATTGTTTGgtaagtcaaa ... tttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactttctgttagcaaggacgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATT
                                tattaat  putative branch site (score: 2)
                                      ttttttgtttccttc  CT-rich tract
                           aacactattaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtctgactaggagtaggagttcacttttgttatccatgtgacatagactttctgttagcaaggacgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATT

- -ctgacta
- - - - - - - - - - - - - - - - - ccatgtg