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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtggatattggcatattttacttttctgaatatttctccataattggtaaatattggcaatttagcatatctgattttcatatacattctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCATGTATGACTATGTTGTCAAGGAGTTGCCAAAGCTTCTGAGCGATAATTT

Basic information

species Glycine max
transcript GLYMA10G15910.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G15910.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g71300.1 (Oryza sativa), 3'ss of exon 3
----ttagtggatattggcatattttacttttctgaatatttctccataattggtaaatattggcaatttagcatatctgattttcatata--cattctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCATGTATGACTATGTTGTCAAGGAGTTGCCAAAGCTTCTGAGCGATAATTT
    | | || ||     ||| |   |   |  || |  || ||   |     || ||||| |     |  || || ||| || |  | ||  |||    ||  |||||| ||||| ||| | ||||| ||| | || || ||||| |||||||||||||||||||||||||| |||||| | |||||  || | || || || ||
gaattcaatgaatgaaatcatttagcatgataatggactttcctttct-----gtgaatatagttggatgtgctta-ctgtttctattttaaccatcaatgagtagGTGCTGGATTCTATTTGAATGCAACAAATGAAAAGTGGAAAAATTGGCGCATGTATGACTATGTTGTGAAGGAGCTTCCAAAAGTTTTAAGTGACAACTT

upper sequence: GLYMA10G15910.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G41530.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------ttagtggatattggcatattttact--tttctgaatatttctccataattggtaaatattggcaatttagcatatctgattttcatatacattctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCATGTATGACTATGTTGTCAAGGAGTTGCCAAAGCTTCTGAGCGATAATTT
                                             || || | | | | | ||||   ||  | | | | ||||       | ||  | |  |  ||  ||  |  || |||   |||| | |    | | ||  ||| || ||||| || ||||||||||| || || || |||||||| ||||| |||||||||||||||||||| ||||||||||| || ||||| || || ||
gtatgcaacgttacatgcttctggtttgcatttcacacacttctttttgtagctttggacctattggtctggtctttaagtatt------cagttaatgatcaagggtgataaaatat-tctttctttcctgtttgatttcgactagGAGCCGGATTCTACCTCAATGCTACTCAGGAAAAGTGGAAGAACTGGCGTATGTATGACTATGTTGTCAAAGAGTTGCCAAAACTCCTGAGTGAAAACTT

upper sequence: GLYMA10G15910.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g09010.t01 (Vitis vinifera), 3'ss of exon 3
----ttagtggatattggcatattttactttt--ctgaatatttctccataattggtaaatattggcaatttagcatat-ctgattttcatatacattctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCATGTATGACTATGTTGTCAAGGAGTTGCCAAAGCTTCTGAGCGATAATTT
     ||     ||   |   |    |  |||   || |  |        | ||| | ||  |  |   ||||  ||   || | ||| |  |   || |  | ||||||| ||||||||||| ||||| ||||||||||| |||||||||||||  ||||||||||||||||||||||| ||||| ||  ||||||| || |||||
gcacctatgaagtagcagtgcacacaagctttggttggaagt------gaacttgtttaaggtatggcttttaaaatgcactcagttttacgt-ttttttcaaccagGTGCTGGATTTTATCTTAATGCCACACAAGAGAAGTGGAAGAATTGGCAGATGTATGACTATGTTGTCAAGGAATTGCCCAAAGTTCTGAGTGAAAATTT

upper sequence: GLYMA10G15910.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ11689 (Selaginella moellendorffii), 3'ss of exon 3
ttagtggatattggcatattttacttttctgaatatttctccataattggtaaatattggcaatttagcatatctgattttcatatacattctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCATGTATGACTATGTTGTCAAGGAGTTGCCAAAGCTTCTGAGCGATAATTT
                          |   |   | | ||   |  || | ||| |     |  || |  | | ||  |||    |   ||||    ||||||| || |||||||||||||| || ||||| |||||||| || ||||| |||||||||||      ||||||| | ||| | || ||  ||   | |||
-------------------------gtgtaggcgagtgctttttgcttcgcaaaaacaattaccttggtttctttggctttttctttttttct----cagGTGCCGGGTTTTATCTCAATGCAACTCAAGAAAAATGGAAAAAGTGGCGAATGTATGACTACTGCACCAAGGAGCTTCCAGAACTCCTCCGCTCCAGTTT

upper sequence: GLYMA10G15910.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ22464 (Selaginella moellendorffii), 3'ss of exon 3
ttagtggatattggcatattttacttttctgaatatttctccataattggtaaatattggcaatttagcatatctgattttcatatacattctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCATGTATGACTATGTTGTCAAGGAGTTGCCAAAGCTTCTGAGCGATAATTT
                             ||| | || || |  ||     ||| | ||||   || |  ||| ||  |||    |   || |    ||||||| || |||||||||||||| || ||||| || ||||| || ||||| |||||||||||      ||||||| | ||| | || || |||   | |||
------------------------gcgagtgatttttgcttcgcaa-----aaacaatggc--cttggtttatttggctttt---tcttttttttctcagGTGCCGGTTTTTATCTCAATGCAACTCAAGAAAAGTGGAAAAAGTGGCGAATGTATGACTACTGCACCAAGGAGCTCCCAGAACTCCTCAGCTCCAGTTT

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|208037065|gb|GD833146.1|GD833146
EST:     CTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: CTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|192325489|gb|FK018415.1|FK018415
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|4313455|gb|AI460574.1|AI460574
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|20448581|gb|BQ252705.1|BQ252705
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|193658696|gb|FK604663.1|FK604663
EST:     GAGGCTTGAATGTGG-AGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|208258359|gb|GE056304.1|GE056304
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCGGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|208102881|gb|GD900871.1|GD900871
EST:     GGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|20449040|gb|BQ253164.1|BQ253164
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCA
EST: gi|192300689|gb|FG989661.1|FG989661
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|20449563|gb|BQ253687.1|BQ253687
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|23064501|gb|BU579274.1|BU579274
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|208137604|gb|GD938954.1|GD938954
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCGGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|193382069|gb|FK346190.1|FK346190
EST:     GCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
EST: gi|207765845|gb|GD737250.1|GD737250
EST:     GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAG                         GTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA
genomic: GAGGCTTGAATGTGGAAGGAGAAGCAGACAGCTGGGACCTTGGAGCAGgtatgccaca ... tctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggtaaatattggcaatttagcatatctgattttcatatacattctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCATGTATGACTATGTTGTCAAGGAGTTGCCAAAGCTTCTGAGCGATAATTT
                          atctgat  putative branch site (score: 4)
                               attttcatatacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtggatattggcatattttacttttctgaatatttctccataattggtaaatattggcaatttagcatatctgattttcatatacattctggaacagGTGCAGGATTTTATCTCAATGCTACACAAGAGAAATGGAAGAATTGGCGCATGTATGACTATGTTGTCAAGGAGTTGCCAAAGCTTCTGAGCGATAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - ttctcca