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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGGCAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataatatattgttatctctacgattcatttgacttccgatgcgctctcttatctttcctccgaataattttatcgtcaaaacttttatccttgt...

Basic information

species Glycine max
transcript GLYMA04G01840.8
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01840.8 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G066528_T02 (Zea mays), 5'ss of exon 3
AGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGGCAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgt-aattataatatattgttatctctacgattcatttgacttccgatgcgctctcttatctttcctccgaataattttatcgtcaaaacttttatccttgt
                      |    | |   | |||   ||||||| ||| || || |||||||| ||||||||||| || || |||||||| ||||||| | || || |  ||  |     ||    |||    | | |  |      | | ||||  |   |  |      ||| ||                    
----------------------GCTCTCGGTGAGGAAGACCAAGGCAGAGAAGGACCCAAACAAGCCCAAGAGGCCTCCGAGCGCGTTCTTCGTCTTCATgtgagttttattggatcatgcggccttttgttctcccgccgtttgg---attttgttatgatcggttgggtctgatttttcag------------------

upper sequence: GLYMA04G01840.8 (Glycine max), 5'ss of exon 3
lower sequence: AT1G20693.3 (Arabidopsis thaliana), 5'ss of exon 3
AGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGGCAGCG---AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataatatattgttatctctacgattcatttgacttccgatgcgctctcttatctttcctccgaataattttatcgtcaaa--acttttatccttgt---
     |   |||  ||| |    |||   || ||    || || || ||    || || || ||||| |||||||||||  | |||||||||||||||||||||||||  |           |  |||  | |||| | |  ||||   |      ||| | || ||    || | |||| || ||     |||   |  | | |   
---CTGTGACCAAGAAGCCGGCTAAAGGAGCAGGGCGTGGCAAAGCTGCTGCTAAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcct----cgcctcaaattctttggttcagtag-tttccatggatacaacttttattgccgtacaaaagttttttcatctggttactgccaatcatttttt

upper sequence: GLYMA04G01840.8 (Glycine max), 5'ss of exon 3
lower sequence: AT1G20696.2 (Arabidopsis thaliana), 5'ss of exon 3
AGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGG---CAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattat---aatat--attgttatctctacgattcatttgacttccgatgcgctctcttatctttcctccg---aataattttatcgtcaaaacttttatccttgt
          | |   ||||| ||| || ||       |  || |   | || |||||||| ||||| || ||||||||| | ||||| |||||||||||||||||||  |   ||| |  | | ||||||||       | |||   |  | | |  |    || ||||  || |   || | ||||   ||    |||||         
-------GCTCTCTGTGACTAAGAAGCCTGCTAAGGGAGCCAAAGGTGCTGCTAAAGATCCAAACAAACCTAAGAGGCCTTCCAGTGCCTTCTTCGTTTTCATgtaatccttcgaatcttcacttttatctctgtttagtacttgtggtttgtttctatggaataactttattctggtaaaaagtttttgagtattgactttg--------

upper sequence: GLYMA04G01840.8 (Glycine max), 5'ss of exon 3
lower sequence: Vv04s0044g00110.t01 (Vitis vinifera), 5'ss of exon 2
AGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGGCAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataatatattgttatctctac--gattcatttgacttccgatgcgctctctta-tctttcctccgaataattttatcgtcaaaactt--ttatcctt-gt---------
| || |||||  ||      |  ||  | ||    |||| |||||| |  || ||||| |||||||| ||||||||| | ||||| ||||||||||||||||| | |   |   | |  |  |  ||  |||   |     || |  | || | | |   | |||  |   |   ||| |   || | ||  |  |||||||| ||         
AAGGTGCCGCTGCCGTCGGAAAAAAGACGGCTAAGAAGGAGAAGGCTGTAAAGGATCCAAACAAGCCGAAGAGGCCTGCTAGTGCCTTCTTCGTTTTCATgtactgaatctcgctagaaacgttgaccagatctgtcattttttccttccgatttttaggttttttatttaatccattctgatgtgagaatctctttatccttcgttgaatgaag

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|193340893|gb|FK307170.1|FK307170
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACA
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACA
EST: gi|208237516|gb|GE032584.1|GE032584
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|207692237|gb|GD676142.1|GD676142
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|208045399|gb|GD841599.1|GD841599
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|193546645|gb|FK503648.1|FK503648
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|193434275|gb|FK399321.1|FK399321
EST:     AAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAAC
genomic: AAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTT-CGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAAC
EST: gi|193592416|gb|FK545634.1|FK545634
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|207761877|gb|GD734150.1|GD734150
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|193629203|gb|FK578151.1|FK578151
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|193621980|gb|FK569216.1|FK569216
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|207832519|gb|GD802663.1|GD802663
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|207717965|gb|GD698319.1|GD698319
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGCGTTCAACAAGGAACATCCCGACAACAAAG
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAG
EST: gi|207785780|gb|GD757879.1|GD757879
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTG
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTG
EST: gi|207690945|gb|GD671567.1|GD671567
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGG
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGG
EST: gi|193535155|gb|FK491699.1|FK491699
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|208196615|gb|GD994910.1|GD994910
EST:     AAGATCCTAACAAGCCAAAGAGGCTTCCTAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAGATCCTAACAAGCCAAAGAGGCCTCC-AAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|208205358|gb|GE004089.1|GE004089
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|207763040|gb|GD731171.1|GD731171
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
EST: gi|193455897|gb|FK417018.1|FK417018
EST:     AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCAT                         GGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT
genomic: AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataa ... gtaattaaagGGAGGAATTCAGGAAGGTGTTCAACAAGGAACATCCCGACAACAAAGCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGGCAGCGAAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataatatattgttatctctacgattcatttgacttccgatgcgctctcttatctttcctccgaataattttatcgtcaaaacttttatccttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG