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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcataatcatatatatattagattacgtctgtcagtctacaacaatgatagttttaatagatagattatactaacatactttgtgtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA

Basic information

species Glycine max
transcript GLYMA09G39090.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 2
-----ctcataatcatatatatattagat-tacgtctgtcagtctacaacaatgatagtt-ttaatagatagattatactaacatactttgtgtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
       |||    ||     |   |  | | | ||   ||   || || ||    | || ||  |    | |  ||  |   ||||| | | | || |      |||| | ||||||||| || || || || ||||||||||||||||| ||||||||||| || |||||||||||||| |||||||| ||  | ||||||||  
ttttctgcattgctatggtggtgccacttgttcatcatccatcttataaaaaaagaacttgttgttcagcaaa--atgatgg-atactatttatttgaca----tagGTAAGGGAGATGCCAAATGTTTTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATCACGATATTGCAGT

upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g38900.1 (Oryza sativa), 3'ss of exon 3
ctcataatcatatatatattagattacgtctgtcagtctaca--acaatgatagttttaatagatagattatactaac-atactttgtgtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
   ||| || | ||| |  | |||    ||||||  ||  ||  |  || | | |    |  |||  ||   | | |  |||||||   ||      |  ||||||   |||||||| || || || || ||||||||||||||||||||||||||||| || ||||| ||||| || || || ||  |  | ||||||||| 
--gatactcttctattttcttgatgtattctgtcgttcagcatgatgattaaactagagaatgatcaatgtcattgattatacttttactgctcactca-cagGTGCGTGAGATGCCGAATGTATTAATTCTTCCTCGAAGTGCAGATTACAGTGAAGAAGTGTGGATTGAAATCAGAGAAAAGGCACTCGCAATATTGCAAT

upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------ctcataatcatatata----tattagattacgtctgtcagtctacaacaatgatagttttaataga---tagattatact-aacatact-----ttgtgtgtgtctgcgt-cagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
                                                                                       || |||||  | |         | |||       |||  ||| |        |  || |  |||   || ||| |  | | || | |      ||    |   || || ||||||  ||||||||| || || || || ||||| || |||||||| ||||||||||| || |||||||||||||| |||||||| ||| |||| || ||  
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT

upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G418294_T01 (Zea mays), 3'ss of exon 3
--ctcataatcat-atatatattagattacgtctgtcagtctacaacaatgatagttttaatagatagattatactaacatactttgtgtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
   |   | |  | ||   |  |  | |     |       || || | | ||  ||  || | ||   |||     || |  | |||||   |      ||||||   |||||||| || || || || ||||||||||||||||| ||||||||||| || |||||||| || || |||||||| ||  | ||||||||  
actttgcacttgtgatgcttgctgtacttataatacgctaatagaaaagtcatgtttcaaacaaatgatttaat---acttgttatgtgttcattgatcacagGTGCGTGAGATGCCAAATGTATTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAGATCAGAGAGAAAGCAATCGCAATATTGCAGT

upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G476107_T02 (Zea mays), 3'ss of exon 4
ctcataatcatatatatattagattacgtctgtcagtctacaacaatgatagttttaatagatagattatactaacatact--ttgtgtgtgtctgcgt-cagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
    |  ||  | |||             |||| | | ||  ||  | || |||| | || ||    |  |  ||  |  |   ||    |  ||| || ||||||  ||||||||| || || || || ||||| || |||||||| ||||| ||||| || |||||||||||||| |||||||| ||| |||| || ||  
---gtcctcgcagataaggacacgagttgctgttattttaacaccgttattgtttcattacattttgttcagcaaactggtgactgatcattgctgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGCGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT

upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G394945_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------ctcataatcatatata----tattagattacgtctgtcagtctacaacaatgatagttttaataga---tagattatact-aacatact-----ttgtgtgtgtctgcgt-cagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
                                                                                       || |||||  |||         | |||       |||  ||| |        |  || |  |||   || ||| |  | | || | |      ||    |   || || ||||||  ||||||||| || || || || ||||| || |||||||| |||||| |||| || |||||||||||||| |||||||| ||| |||| || ||  
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT

upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
------------ctcataatcatatatatattagatt-acgtctgtcagtctacaacaatgatagttttaatagatagattatactaacatactttgtgtgt-gtctgcgt--cagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
             |   | | |  || |  | | |||  || ||| |  |   |     | ||  | ||  |   | | |||| ||  ||| | || | | | || | | |  ||||||||||| ||||| || ||||| || || ||||| ||||||||||||||||| || || |||||||| ||||||||||| ||||| ||||| |||||  
gtatgactttcttttccagtgac-taaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgttgtttatcctg-catccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT

upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
ctcataatcatatatatattagattacgtctgtcagtctacaacaatgatagttttaatagatagattatactaacatactttgt-gtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
   | ||| | |||   || | |  |  | | | |      ||||||  |   ||  |||   ||   ||  |||    |    |  ||  | ||| |||||| || || ||||| || || ||||| ||||| || ||||||||||| |||||||| ||||||||||| |||||||||||| |||| | |||||| || |
ggaaaaataaaatagccat-acacaatattttttatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA

upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
-------ctcataatcatatata-tattagatt-acgtctgtcagtctacaac----aatgatagttttaatagatagattat-actaacatactttg--tgtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
          ||  |||| | |  ||  || || ||   |   | |  |  |     ||| | |  |  ||| |||   | || | | |  |  |     | | |||||    ||||||| ||| ||||| ||||||||||| |||||||| ||||| |||||||||||||| || |||   || ||| |    |||||  | ||| |  ||    
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT

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|151408973|gb|EV278781.1|EV278781
EST:     CTGGATGTGCTTTGGATGGGGCAGAAGGGCCTCAATGGATGGAAGCATGG                         GTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGT
genomic: CTGGATGTGCTTTGGATGGGGCAGAAGGGCCTCAATGGATGGAAGCATGGgtacggtaaa ... tctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGT
EST: gi|9986317|gb|BE660425.1|BE660425
EST:     CTGGATGTGCTTTGGATGGGGCAGAAGGGCCTCAATGGATGGAAGCATGG                         GTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGT
genomic: CTGGATGTGCTTTGGATGGGGCAGAAGGGCCTCAATGGATGGAAGCATGGgtacggtaaa ... tctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGT
EST: gi|8283239|gb|BE020800.1|BE020800
EST:     CTGGATGTGCTTTGGATGGGGCAGAAGGGCCTCAATGGATGGAAGCATGG                         GTGAAGGAGATGCCTAACGTGTTGATACTTTCTCGAAGTGCAGATTACAGT
genomic: CTGGATGTGCTTTGGATGGGGCAGAAGGGCCTCAATGGATGGAAGCATGGgtacggtaaa ... tctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatagttttaatagatagattatactaacatactttgtgtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
                        tactaac  putative branch site (score: 0)
       ttttaatagatagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcataatcatatatatattagattacgtctgtcagtctacaacaatgatagttttaatagatagattatactaacatactttgtgtgtgtctgcgtcagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - tctgtca
- - - - - - - - - - - - - - - - - -gtctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg