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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaggtgaaggtattaattatttcttattcatcctccaaccaaaaagcaaaaatctaaaaaaacaaatgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG

Basic information

species Glycine max
transcript GLYMA19G02360.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
gtatgtaggtgaaggtattaattatttcttatt--catcctccaaccaaaaagcaaaaatctaaaa------aaacaaatgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG
||||| |        |   ||| |   | ||||   |   | ||   | |  | || | ||| | |      ||| |    |||  |||| |||||||| || || |||||||||||||| || |||||||| |||||||| || || ||||||||||||||  |||| |||||||| ||||| ||||
gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG

upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
---gtatgtaggtgaaggtatta-attatttcttattcatcctccaaccaaaaagcaaaaatctaaaaaaacaa---atgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG
      | || ||    | |||  ||||  | ||   || |   | |   | |      ||| |   | |  |    |   ||  |||| |||||||| || || || |||||||| |||||||||||||| ||||  || || || || || || |||||  |||| |||||||||||||||||||
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG

upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
gtatgtaggtgaaggtattaattatttcttattcatcctccaaccaaaaagcaaaaatctaaaaaaacaaatgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG
    ||| |  |   |||| |    ||   | |  || | ||  ||||        || |   || | |  | |||  |||| || || || || || ||||||||||||||||| |||||||| |||||||| || || |||||||| || || || || |||||||||||||| ||||
----gtaagcaactatattgaaatgttaaaaatattcattcatacaaatgt-----atttgctaacatattttttt-cagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG

upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtaggtgaaggtattaattatttcttat--tcatcctccaaccaaaaagcaaaaatctaaaaaaacaaat---gtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG
          | | ||||   ||| |  |||   ||| | ||  |   |   |||||  | | ||  || ||||    ||   |||| |||||||| || || || |||||||||||||||||||||| |||||| |  |  || || ||||| ||||| || |||||||| |||||||| ||||
----------gtacgtatctcttactctttaggatcaacatcttat--atttgcaaattttttaaccaataaatcccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG

upper sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtaggtgaaggtattaatt-----atttcttattcatcctccaaccaaaaagcaaaaatctaaaaaaacaaatgtt-----tatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG
||||||  |  |     ||||       |  ||   |   ||||    |   |     | ||  |  | ||| ||||| |     |  ||||||| ||||| ||||| ||||||||||| ||||| ||||||| ||| || | | | ||  | || ||||| ||  |||| |||||||| ||||||||||
gtatgtctgaaagccacttaacccgataacctcaactctgtcctttctctctatgtttataaattttagaaaaaaatgctcccattgcagGAATATAATGCAAAGCTCTCTGATTTTGGGCTTGCAAAAGATGCTCCAGACGAGAAAAAATCCCACGTATCAACCCGAGTCATGGGAACTTATGGTTATG

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|23063935|gb|BU578708.1|BU578708
EST:     GGCCCATAATATATCGTGATTTCAAAACATCTAATATACTATTAGATGCG                         GAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAG
genomic: GGCCCATAATATATCGTGATTTCAAAACATCTAATATACTATTAGATGCGgtatgtaggt ... atgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAG
EST: gi|23733669|gb|BU765039.1|BU765039
EST:     GGCCCATAATATATCGTGATTTCAAAACATCTAATATACTATTAGATGCG                         GAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAG
genomic: GGCCCATAATATATCGTGATTTCAAAACATCTAATATACTATTAGATGCGgtatgtaggt ... atgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttattcatcctccaaccaaaaagcaaaaatctaaaaaaacaaatgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG
                               atctaaa  putative branch site (score: 3)
                    aaaaagcaaaaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaggtgaaggtattaattatttcttattcatcctccaaccaaaaagcaaaaatctaaaaaaacaaatgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA