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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccagaaaattgtcaatattttgattttgttttcttctattgataagattataattgtaatattcagttgagttcatgaaaaatttgattaatgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

Basic information

species Glycine max
transcript GLYMA02G11320.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
ccagaaaattgtcaatattttgattttgttttctt-ctattgataagattataattgtaatattcagttgagttcatgaaaaatttga--ttaatgttt-gcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA
   ||  ||  |  || |||| || |  || |  | ||  | || | |    |  ||   |||| | ||||  |  | | |  |||||   |  ||||| ||||  ||  |  ||||| ||||| || |||||||| ||||||||||  || |||||||||||||| || || |||||||| ||||||||||||||||| |   
-ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctg--gtattga-ttgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT

upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g30060.1 (Oryza sativa), 3'ss of exon 5
--ccagaaaattgtcaatattttgattttgttttcttctattgataagattataattgtaatattcagttgagttcatgaaaa-atttgattaatgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA
         ||| |       |  | | |||| |     | | ||| |  |||  |  | | |||  ||  | ||  |  |   ||| | ||    | | |||   |  ||  |  | || || || || || || || |||||||  ||||||||||||||||| || || |||||||||||||| ||||| |||||||| |
ttttgatgtattataggatgctgaaatctgttctgcatgaatcatatg-ctatgttattgaaatt--gtaaaatttgtatacttattagtttcccctctccagCAATCACGTCCTATAACCAAGTTTACAGAGGACTTCGATTTCATGGCAATGAATGAGAAGTTTAACAAAGATGAAGTATGGGGCCATCTCGGTAAAAGCA

upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 5
ccagaaaat-tgtcaatattttgattttgttttcttctattga-taagattat--aattgtaatattcagttgagttcatgaaaaatttgattaatgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA
  ||  | | | |  |||  |||        | ||   ||||| ||| ||| |  ||| || | ||   ||    ||  |  |   ||  ||     |||||||  ||  |  || || |||  |||||||||||| ||||||||||| || |||||||||||||| || || |||||||||||||| ||||||||||| |   
-gagggagtatttgtataccttgggaaatgatgctaggattgaataatattgttaaatagttaaat---gtcagatttgttgatgtttgtatcttgctttgcagTTTTCACAGTCTGTAACAGCATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTATGGGGCCATCTTGGTAAGAAAT

upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G051622_T02 (Zea mays), 3'ss of exon 5
ccagaaaattgtcaatattttgattttgttttcttctattga-taagattataattgtaatattca---gttgagttcatgaaaaatttgattaatgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA
   ||  ||| |  |||  |||        | |||  ||||| ||| |||     |  |||| | |   ||    ||  | ||   ||  ||     |||||||  ||  |  ||||| |||| |||||||||||| ||||||||||| || |||||||||||||| || || |||||||| |||||||||||||| || |   
---gagtatt-tgtataccttgggaaatgatgcttggattgaataatatttgttgttaaatagttaagtgtcagatttgttaatgtttgtatcttcctttgcagTTTTCACAGTCAGTAACAACATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGAAAGAAAT

upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G341027_T01 (Zea mays), 3'ss of exon 5
ccagaaaattgtcaatattttgattttgttttct-tctattgataagattata-attgt-aatattcagttgagttcatgaaaaatttgattaatgtt-----tgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA
         |   |||   |   || |||||||  ||  ||||  | ||| |   ||||  |  | |  ||   |  |    |   || | |    ||     | |||   |  |   |  | || || ||||| || || ||||||||||  |||||||||||||||||||| || |||||||||||||| |||||||||||||| |
--------cttaaaatgcctctgttctgttttcagtcccttgaggacattctttgttgtcgacttgcttttttttaaactgtagtcttcactgtcattctctctacagCAATCGCATCCCATAACCAAGTTCACAGAGGACTTTGATTTCATGGCAATGAATGAGAAGTTCAACAAAGATGAAGTATGGGGCCATCTTGGTAAAAGAA

upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
-------------------ccagaaaattgtcaatattttgattttgttttcttct-------attgataagattataattg----taatattcagttgagttcatgaaaaatttgattaatgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA
                      | | | ||| |     || ||||  ||||            ||  |  || ||| ||| |    | |  || ||    ||     || ||||   ||  |||| |||| | |  | |  ||| |  ||||||||||||||||||||||||||||||||||| || |||||||| |||||||||||||||||||||||||| || ||||
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattc--ttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA

upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
ccagaaaattgtcaatattttgattttgttttcttctattgataagattataattgtaatattcagttgagttcatgaaaaatttgattaatgt-ttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA
| |  | |   |  || || ||       | | | | ||   |      | ||||  | |    | ||||   |||| || |||| |    ||  |||||||| |  ||  |||| |||||||||||||| |||||||||||||  |||||||||||||| ||||| |||||||||||||||||||||||||||||| |||
ctattataggtttgattttatggggagaatatttgcaatgagtttctccaaaatta-attggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA

upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S198_51V6.2 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------ccagaaaattgtcaatattttgattttgttttcttctattgataagattataattgtaatattcagttgagtt----catgaaaaatt--tgatta-----atgtttgcagG--GTTTCCGCTC---AGTCACAA-----AATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA
                                                                              || |  |   |||  | | ||| ||   || |  | |   || | |     |  || ||    |||||||      ||    |||  |||| |     |   ||| |    ||||| |||    | || ||      |||||||||||||||| || |||||||| ||||||||||||||||| ||||| ||||| |||||    || ||   ||   
gtaattttttatactttcctaaggttttaaggccccgtttgttcttgtttcaacttacaggttatactggcactaattgatatctaataattgtctcattgtgcactcgttaactctcaaaagttggcatccaacatcttcttgagttgttctgtgtctcattcctgatcatgacgaaacttgtaacttgtttcagCTGGCGAATCCCACGCAGCAATTCACTGAAGATTTCGACTTCACAGCCATGAATGAGAAGTTCAACAAGGACGAAGTTTGGGGAACGCTCGGAGGAAAGG

upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S35_195V6.1 (Physcomitrella patens), 3'ss of exon 7
ccagaaaattgtcaatattttgattttgttttcttctattgataagattataattgtaatattcagttgagttcatgaaaaatttgattaatgtttgcag-
        ||||     ||  |||| |  |  || || |  |      ||   | |||  |    |    ||  ||||   || || ||     |||      |   | |   | || || |     |||||| ||||||||||| |||||||| |||||||||||||| || ||||| ||||| |||||    |||||   ||   
------tgttgtttggtttccgattatagta-ctactttcaagtttcatactttcgtagcaagacgagtggtcaatgattgatgtggttgtcaattgtgataagcagCTGGCGAATCCCACACAGCAATTCACAGAAGATTTTGACTTCACAGCCATGAATGAGAAGTTTAACAAGGACGAAGTTTGGGGAACCCTTGGGGGAAAGG

upper sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S35_182V6.2 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------------------------------------ccagaaaattgtcaatattttgatttt---gttttcttctattgataagat------tataattgtaatattcagttgagttcatgaaaaatttgattaatgtttgcag-
                                                                          |     | || |     |  ||||      |   | | | | |   ||  |      | |   ||||  || || | | ||  |||    ||  | ||  |  |||      |   | |   | ||  | |      |||||||||||||| || |||||||| ||||||||||| |||||||| || ||||| |||||    |||||    |   
gcaagtggcgattcttggtctccctcttctaattcgccttttcattttggaatattactatctagatttggattctgctgagttatttccttcctgatcacagcgcactttgcaacttccaacttgctgtgtgtgtctgtagcatacaat-gggtctatgtctgataaggttgttacttgtgataagcagCTGGCGAATCCTACACATCAGTTCACTGAAGATTTCGACTTCACAGCCATGAATGAGAAATTCAAAAAAGACGAAGTTTGGGGCACCCTTGGAGGGAAGG

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|13790679|gb|BG653270.1|BG653270
EST:     ATCATCATGGCTATAGTTATAGAGGACGTGGAAGAGGAAGAGGAACTGGG                         GGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATG
genomic: ATCATCATGGCTATAGTTATAGAGGACGTGGAAGAGGAAGAGGAACTGGGgtaactttca ... atgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATG
EST: gi|26269440|gb|CA820503.1|CA820503
EST:     ATCATCATGGCTATAGTTATAGAGGACGTGGAAGAGGAAGAGGAACTGGG                         GGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATG
genomic: ATCATCATGGCTATAGTTATAGAGGACGTGGAAGAGGAAGAGGAACTGGGgtaactttca ... atgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATG
EST: gi|10709997|gb|BF009721.1|BF009721
EST:     ATCATCATGGCTATAGTTATAGAGGACGTGGAAGAGGAAGAGGAACTGGG                         GGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATG
genomic: ATCATCATGGCTATAGTTATAGAGGACGTGGAAGAGGAAGAGGAACTGGGgtaactttca ... atgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattataattgtaatattcagttgagttcatgaaaaatttgattaatgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA
                                        gattaat  putative branch site (score: 3)
                             atgaaaaatttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagaaaattgtcaatattttgattttgttttcttctattgataagattataattgtaatattcagttgagttcatgaaaaatttgattaatgtttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
ccagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaaa