Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

Basic information

species Glycine max
transcript GLYMA18G35450.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
                          |     |||  |   | |  |       | |  | |  || |    ||    || ||  ||   | || |||||||||| ||||| || ||||||||||| || ||||||||||||||||| ||||||||||| || |||||||| ||||| ||||| ||||| ||||||||||
------------------------gtttttggtattgagaaaatcgtatataatactcttcttgaagta--acaatcattggtaattt-ttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

upper sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatt-tctttacaaattttcc------atctttttgtggttgacttttttgt--agGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
    |    ||     ||  | ||       ||| |  |||   | ||| |  |||  | | ||  | | |||       | |  |   ||||    ||| ||||  ||||||| ||||| || ||||||||||| || ||||||||||||||||| ||||||||||| || |||||||| ||||| ||||| ||||| ||||||||||
---gttggtacttggttggttata------gatacagtttttggtattgagaaaatcgtatataatactcttcttgaagtaacaatcattggtaatttttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

upper sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G26840.1 (Arabidopsis thaliana), 3'ss of exon 1
actatcttaaccca--actgactttatctcacaatataaatttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
||| | | |    |  ||  |        ||    ||  | ||||| |||         ||| ||    || |   || || | |   ||  | |||| |||||||| || ||||||||||||||||| || |||||||||||||||||||| |||||||| || |||||||| || |||||||| ||  | ||||| ||||
actctttcaggttactaccaaaagagagccatgtgatttagttattgtttcatatgcggtctctaacgtttattgttccttctata--tgtttgttttatagGATGGAAACGAGGTTTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAGAAGCTGATGAATGCTTACTGTGACCGGCAATCTGTGGACATGAACTCCATTG

upper sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
-actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
    ||      ||  |||  ||  | ||| | |   |   |     ||     |           ||||||       ||| |  ||     ||   |||||||| || ||||| ||||||||||| ||||||||||| ||| |   ||| || |||   || || |||||||| || || || || || ||||| ||||
atggatgactctcctcctgttttcttttca-actcctagcattcccattcccccaccccacaagtgaatttttgtaaaatttttattttgtggttgcatagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG

upper sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0059g01310.t01 (Vitis vinifera), 3'ss of exon 1
actatcttaacccaactgactttatctcacaatataa--atttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
        |   | |   | ||   || | |||||     |||    ||||   |  || ||  ||||  |  | |   | | || ||    ||| ||| ||||||| ||||| |||||||| ||||| ||||||||||| ||||| ||||| || ||||| || || ||||| || |||||||||||  | ||||| ||||
-gggagcaagttctaagaatttggactaaaaatatctctgtttgcagtttgctaggtttcctggacaagatgacgaggatgt-gttgtgttttttattgcagGATGGGAATGAAGTTTTCTTCAGGATCAAAAGAAGCACACAGCTGAAGAAGCTCATGAATGCTTATTGTGACCGACAATCTGTAGACCTCAACTCGATTG

upper sequence: GLYMA18G35450.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
-------------actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
              || |  |   |      ||||   |       ||   | ||        | |||||| |||| |||| |||     |||| ||||||       |||||||||| || ||||| ||||||||||| ||||||||||| ||| |   ||| || |||   || |||||||||||||| || || || || ||||| ||||
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaattttttta-aaatgttc-----ttttctggttg-------tgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG

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|213604768|gb|DB956109.1|DB956109
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|151395673|gb|EV265550.1|EV265550
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|151399595|gb|EV269466.1|EV269466
EST:     AGAAGCCTTCTGATCAAGGAGCGCATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|192310968|gb|FG998916.1|FG998916
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|24136264|gb|BU926774.1|BU926774
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|213612132|gb|DB974552.1|DB974552
EST:     CAAAGTCAAGGGCCAG                         GATGGCAATGAATTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: CAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|193536500|gb|FK489222.1|FK489222
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTT-AGGATTAAAAGA-GCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|151407669|gb|EV277484.1|EV277484
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|192310967|gb|FG998915.1|FG998915
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|192308691|gb|FK000081.1|FK000081
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|192319169|gb|FK009109.1|FK009109
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTTAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtcacaattc ... ttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
                                      ggttgac  putative branch site (score: 4)
                                            cttttttgt  CT-rich tract
        aatttctttacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actatcttaacccaactgactttatctcacaatataaatttattttttgggggaatttctttacaaattttccatctttttgtggttgacttttttgtagGATGGCAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

- - - - - cccaact
- - - - - - - - - - - - - - - - - - - - - - - - gggggaa