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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actctctgtgcttcgttgggttctcgtgtcttgtagatggtttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA

Basic information

species Glycine max
transcript GLYMA01G25940.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g26970.1 (Oryza sativa), 3'ss of exon 2
actctctg---tgcttcgttgggttc-tcgtgtcttgtagatggtttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
| |   |    | || | ||           |||    | || | |||  ||||  |||| | | |    |  ||||| |        |||    || |  ||||||| |||||||| || ||||||||||||||||| ||||| ||||| || || ||||||||||| 
atttattagattcctccattacacaggctaggtccataaaattgcttggttcctccaatgcaagct----taataattttgcaaaatatttggtgttgtaacagCTGCTAATGGAGTAGTTATTGCCACCGAGAAGAAGTTGCCTTCTATTTTAGTGGATGAAACATCT

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 2
actctctgtgctt--cgttgggttctcgtgtcttgtagatggt-ttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
  | | |||  ||   | |  |           ||| |||  | || | | |  |  | ||   |    |  | ||| |  | |   ||| | || ||||||||||| ||||| || || || ||||| |||||||||||||| ||||| || || ||||||||||| 
-ttttgtgtagttactgctcagagactacagtctgttgattctcttcagttccct--tttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCT

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 2
actctctgtgctt--cgttgggttctcgtgtcttgtagatggt-ttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA-----------------------------------
  | | |||  ||   | |  |           ||| |||  | || | | |  |  | ||   |    |  | ||| |  | |   ||| | || ||||||||||| ||||| || || || ||||| |||||||||||||| ||||| || || |||||||||||                                    
-ttttgtgtagttactgctcagagactacagtctgttgattctcttcagttccct--tttagcctagtttattgattctgaggtatatttgttatgtttgcagCTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCTGTAAGTCTAACATCACTCTTAATGCTGAATTCCTC

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G824831_T04 (Zea mays), 3'ss of exon 3
actctctgtgcttcgttgggttctcgtgtcttg--tagatggtttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
      ||| ||  ||    | |  |   ||||  |||   ||   |    | |  | ||  |     |  |  |||  |      | | | || ||||||||||| ||||| || ||||||||||| ||||||||  |||| ||||| || || ||||||||||| 
--ataatgttctatgtaatatacatggtccttggttaggcagtacaaccattttgttttacttctgcctctttgttaattccgaaatatatcatgtttgcagCTGCCAATGGTGTAGTCATTGCCACTGAGAAGAAGCTGCCTTCTATTTTAGTGGATGAAACATCT

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G850355_T05 (Zea mays), 3'ss of exon 2
-------actctctgtgcttcgttgggttctcgtgtcttgtagatggtttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
        |  ||| |  ||  |    ||   || |    |||   |||  |    | || | ||  ||||   | |  || |   ||     | | || ||||||||||| || || || || |||||||||||||||||| |||| ||||| || || ||||||||||| 
tgccataccagtctttttttaatcaaattgctgtat----taggcagttcaaccattttattttac-ttgtgcatct--ttgttaattctacatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 2
actctctgtgcttcgttgggttctcgtgtcttg--tagatggtttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
   || ||| ||  ||    | |  |    |||  |||   ||   |    | || | ||  |     |  |  |||  | |    | | | || ||||||||||| || || || || |||||||| ||||||||| |||| ||||| ||||| ||||||||||| 
--gctgtgttctatgtaatatacatggtcattggttaggcagtacaaccattttattttacttgtgcatctttgttaattctgaaatatgtcatgtttgcagCTGCCAACGGTGTAGTGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 3
actctctgtgcttcgttgggttctcgtgtcttgtagatggtttgaatcctgtaatgtatgttgtagttg-taattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
           ||  ||   |  ||   ||   |    |    ||    | ||| | |  ||||  ||| |||| ||   | | |||||   ||| ||||||| ||||||||||||||||||| || || |||||| | || |||||||||||||||||| | || 
----------gttttttcaatgatctaatcaaattcgagag--gagatttttaaggaacattgtctttggtaatcatgactgttgttttc--tttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G16470.2 (Arabidopsis thaliana), 3'ss of exon 2
actctctgtgcttcgttgggttctcgtgtcttgtagatggtttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
              ||| |    |    |  || |  || ||  |   |  | |   || |||||| | |  |   ||   | | |||   ||  ||||||| | ||||||||||||||||| || || ||||| ||||| |||||  ||||||||||| |||| 
--------------gtttgtcaatgtcatgatgaaattgtttatagatcaatgaaaaat-ttgtagatttcttctgataacttggtttc--ttactgcagCTTCTAATGGAGTTGTCATTGCAACTGAAAAGAAGTTGCCTTCTATTCTGGTTGATGAAGCATCT

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|4397406|gb|AI496403.1|AI496403
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|193466029|gb|FK429770.1|FK429770
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTG
EST: gi|58014614|gb|CX701356.1|CX701356
EST:     CATGCC-TGNACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: CATGCCTTG-ACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|120494647|gb|EH222814.1|EH222814
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|18690708|gb|BM519556.1|BM519556
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|208121904|gb|GD918927.1|GD918927
EST:     CCTTGACAGCTGTTGGCTCTGGACAGACGTTCGTTTGGGAAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTG
genomic: CCTTGACAGCTGTTGGCTCTGGACAGACG-TC-TTTGGG-AATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTG
EST: gi|14259203|gb|BG882111.1|BG882111
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|9564578|gb|BE474087.1|BE474087
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|19052912|gb|BM731579.1|BM731579
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|7925135|gb|AW831161.1|AW831161
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|298198188|gb|HO039727.1|HO039727
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|15204528|gb|BI427296.1|BI427296
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|151406778|gb|EV276593.1|EV276593
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
EST: gi|24206299|gb|BU965552.1|BU965552
EST:     GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAG                         CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG
genomic: GCATGCCTTGACAGCTGTTGGCTCTGGACAGACGTCTTTGGGAATAAAAGgtaattgatt ... atttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA
                                        ttttaat  putative branch site (score: 3)
                                              tttttgc  CT-rich tract
                     ttgtaattatatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actctctgtgcttcgttgggttctcgtgtcttgtagatggtttgaatcctgtaatgtatgttgtagttgtaattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA

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