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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttatttcagctcagcattcatgaaaatgtcatactttgtttttataatcttgcatttggcatggaggcaaaacattgcttagttacattagcagac...

Basic information

species Glycine max
transcript GLYMA02G12330.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G12330.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os08g44440.1 (Oryza sativa), 5'ss of exon 2
AATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttatttcagctcagcattcatgaaaatgtcatactttgtttttataatcttgcatttggcatggaggcaaaacattgcttagt-tacattagcagac---
||||||  ||||| ||||| || | ||| |||||  | ||||| || || ||||| || || |||||||||||||||||||||||||||||||  |||  ||   |      | ||   |  ||   |||||||       |  | | | |   |    ||      | ||||     |  | | |        
AATTCAAATGGGATGATGTTAAGGTTGACAAGCACCGAGAGAATTACCTCGGTCATAGCATTAAGGCTCCTGTTGGAAGATGGCAGAAAGgtaaatataacaatac----cccttgtttacatccacctttgttggctggctagtccttataaaacaatggttttttactgctcgacatgaagtggtttttctt

upper sequence: GLYMA02G12330.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G167548_T01 (Zea mays), 5'ss of exon 2
AATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttatt-tcagctcagcattcatgaaaatgtcatactttgtttttataatcttg-catttggca----tggaggcaaaacattgcttagttacattagcagac
||||||  ||||| |||||||| | ||| |||||| ||||||| || |||||||| ||| | |||||||| ||||| ||||||||||||||||  | || ||  || | | | |      |||| || |  |||     |  | ||  |||   |||    |   ||   || ||||    ||   ||        
AATTCAAATGGGACGATGTGAAGGTTGACAAGCATCGGGAGAATTACCTTGGTCATAGTGTTAAGGCTCCGGTTGGTAGATGGCAGAAAGgtaaatgttatccacttatcctgcccttttatgt-atccactgtcccagttgttttttcatactgcacccttctgggtggaatattgaaatgtggtatgtt-----

upper sequence: GLYMA02G12330.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G52220.1 (Arabidopsis thaliana), 5'ss of exon 2
AATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttatttcagctcagcattcatgaaaatgtcatactttgtttttataatcttgcatttggcatggaggcaaaacattgcttagt--tacattagcagac--
|||||| |||||| || || || ||||||||  |||||||||||||| | |||||||||||||| || ||||||||||||||||| ||||||| || ||||   |   || ||  |    | |  || |||||       | || |  ||   | ||  |  | ||   | ||| ||  | ||||         
AATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGGGTCACAGTATCAAAGCCCCTGTTGGAAGATGGCAAAAAGgtactt-tttcttatgtacactctcggtggt-tgttaatttgta--agctaactagttttcatcttgacgatataatcctcctttgtgcttcattgctctgttc

upper sequence: GLYMA02G12330.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv13s0101g00090.t01 (Vitis vinifera), 5'ss of exon 2
AATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttatttcag----ctcagcattcatgaaaatgtcatactttgttt--ttataatcttgcatttggcatggaggcaaaacattgcttagttacattagcagac
|||| |  ||||| ||||| || | |||||| ||  | ||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||   ||| |    |||    || |      |  |||    | ||   ||| | |||| ||| ||     ||      |  |   | | | | | |       
AATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAGgtattaccttctgattcctctatgtttactgttttaacatgaaatattcagttacattctttcatgtgtgtcagacctttcatttgattcactgaaactg------

upper sequence: GLYMA02G12330.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S59_322V6.1 (Physcomitrella patens), 5'ss of exon 2
AATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttatttcagctcagcattcatgaaaatgtcatactttgtttttataatcttgcat-ttggcat-----ggaggcaaaacattgcttagttacattagcagac
| || | |||||| ||||| || || || |||||  | ||||| || |||||||||||  ||||||||||||||||  |||||||||| ||||   | |  |  | |||  |||   | |  |     |||| |    | |   || |  |||  ||     | || |  |   ||  || || |||  || | | 
AGTTTAATTGGGATGATGTCAAGGCCGACAAGCACCGCGAGAATTACCTTGGTCACAGCCTCAAGGCTCCTGTTGGGCGATGGCAGAAGGgtaagaactggaa-taagc--tcagtgagacattgctttttgatcggctgaaagtgaacgttgttattattcgcagtctcactcttcttttgtcacacgagaacag

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|193689769|gb|FK632302.1|FK632302
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|193721331|gb|FK656611.1|FK656611
EST:     CTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: CTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208109444|gb|GD905832.1|GD905832
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208176652|gb|GD975667.1|GD975667
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|193526965|gb|FK484533.1|FK484533
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|193364356|gb|FK333144.1|FK333144
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAAATGCAGAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAA-TGCAGAA
EST: gi|207715987|gb|GD699379.1|GD699379
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|193434699|gb|FK403273.1|FK403273
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTGTACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208027693|gb|GD824523.1|GD824523
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208313744|gb|GE113010.1|GE113010
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208196224|gb|GD992643.1|GD992643
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208078131|gb|GD875747.1|GD875747
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|193516947|gb|FK476057.1|FK476057
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|207745174|gb|GD715906.1|GD715906
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|193401856|gb|FK367075.1|FK367075
EST:     GAACTATCTTGGTCACAGTATCAGGGCTCCTGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|207826755|gb|GD800244.1|GD800244
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208294350|gb|GE093049.1|GE093049
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208140188|gb|GD934810.1|GD934810
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208208607|gb|GE002597.1|GE002597
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAG
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208145203|gb|GD943962.1|GD943962
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|193604270|gb|FK558899.1|FK558899
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|193451219|gb|FK420145.1|FK420145
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208115280|gb|GD910833.1|GD910833
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|208043768|gb|GD841536.1|GD841536
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|298196401|gb|HO041144.1|HO041144
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
EST: gi|193347217|gb|FK311003.1|FK311003
EST:     GAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG                         GGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA
genomic: GAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttattt ... aattcaacagGGAAAGATCTTTTCTGGTATACCAGGGATAAAAAGTCCCAAAATGCAGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAGgtatttatttcagctcagcattcatgaaaatgtcatactttgtttttataatcttgcatttggcatggaggcaaaacattgcttagttacattagcagac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG