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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtccatcactagcaaatttatatacttgtcatttgtgaagttaaaagtttttacatcatatgtattaatatattaatacgttatgttatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCAGTAAGTTTGATCATTTCTTATT

Basic information

species Glycine max
transcript GLYMA11G14980.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G14980.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 4
-ttttgtccatcactagcaaatttatatacttgtcatttgtgaagttaaa-agtttttacatcatatgtattaatatattaatacgtt-atgttatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCAGTAAGTTTGATCATTTCTTATT
 | || |  |    ||      |  | |  |    |||  |     ||   ||     | || | ||| | | | | | || | | || ||||||| |  ||||| || |||||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||  |||||||||||                      
atattatagagt-ttaaggtcatcgtgtgttgacaattattttccctatctagcgaccatatta-atgcacttaca-actattgcattgatgttatgtcacagGTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA----------------------

upper sequence: GLYMA11G14980.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
ttttgtccatcactagcaaatttatatacttgtcatttgtgaagttaaaagttt--ttacatcatatgtattaatatattaatacgttatgttatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCAGTAAGTTTGATCATTTCTTATT
 ||||  ||  | ||     | |   || ||||  ||| |     |     | |  | |  | || | |||| ||  |   |    |  |  ||  || ||||| || || ||||| || ||||| ||||||||||| || || |||||||| |||||||| |||||||||||||||||                       
ctttgctca--attaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaactaactatggttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT----------------------
















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|298167627|gb|HO012890.1|HO012890
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|207784652|gb|GD757759.1|GD757759
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|208089572|gb|GD886161.1|GD886161
EST:     ATCCAAATGGTTATGAGCTTGCAGGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|298194743|gb|HO043215.1|HO043215
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|193389815|gb|FK353580.1|FK353580
EST:     TCCAAAATGGTTATGAGCTTGCGAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: TCC-AAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|193570153|gb|FK525308.1|FK525308
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTC-AGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|14011884|gb|BG726806.1|BG726806
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|298182929|gb|HO028142.1|HO028142
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|193656102|gb|FK606704.1|FK606704
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|298167833|gb|HO013096.1|HO013096
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|193426714|gb|FK391309.1|FK391309
EST:     CCAAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: CC-AAATGGTTATGAGCTTGCAAGTGAGCGCTGGACA-CCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|193517085|gb|FK476125.1|FK476125
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|8286011|gb|BE023499.1|BE023499
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|208224042|gb|GE022585.1|GE022585
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTAATTAGAGTATCATA
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTA-TT-GAGTATCATA
EST: gi|193512345|gb|FK467219.1|FK467219
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|208098942|gb|GD892717.1|GD892717
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         -TAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|298183716|gb|HO028929.1|HO028929
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|208118643|gb|GD917892.1|GD917892
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|208061404|gb|GD859230.1|GD859230
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTA
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTA
EST: gi|193583795|gb|FK543779.1|FK543779
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|208075086|gb|GD876367.1|GD876367
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAAT
EST: gi|298167168|gb|HO010607.1|HO010607
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|16104747|gb|BI892487.1|BI892487
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT
EST: gi|7284473|gb|AW597063.1|AW597063
EST:     ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACG                         GTAGAGAGTATAGTATTGAGTATCATATCAATGCTGTCCAGCCCTAATGAT
genomic: ATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATACGgtacgtgaac ... tatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagtttttacatcatatgtattaatatattaatacgttatgttatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCAGTAAGTTTGATCATTTCTTATT
                             tattaat  putative branch site (score: 2)
                                            ttatctt  putative PPT
      tttttacatcatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtccatcactagcaaatttatatacttgtcatttgtgaagttaaaagtttttacatcatatgtattaatatattaatacgttatgttatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCAGTAAGTTTGATCATTTCTTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG