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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggtttttttacttttcggttaatcgattgaaggaagtgtgattttaaatattcgaaatttcaattgttcgattggaatggtttgtttttggttcag

Basic information

species Glycine max
transcript GLYMA11G19120.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 1
CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggtttttttacttttcggttaatcgattgaaggaagtgtgattttaaatattcgaaatttcaattgttcgattggaatggtttgtttttggttcag--
|||||| | ||||||||||| ||||| ||  | |||||||| ||||| ||||||||||| || || || ||||| || ||||| ||||||||||| || |||||| |  |  |            | |  |||          |  || || | | | ||  |    ||||    |||||    |  |    | |  |  |  
CCCAACATCAAGTGGAACGATGTCGCCGGCCTCGAGAGCGCCAAGCAAGCGCTGCAGGAGGCCGTCATATTGCCTGTCAAGTTCCCGCAGTTCTTTACGGgtgagcggctgctgcgaggataaccagtatattttcattctccttgttgtagagaatagaggt---gattgcaaaattggtggtggatccgatcgtataggcc

upper sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G088834_T01 (Zea mays), 5'ss of exon 1
CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgag----ggttttttta--cttttcggttaatcgattgaaggaagtgtgattttaaatattcgaaatttcaattgttcgattggaatggtttgtttttggttcag
|||||| | |||||||||||||| || ||  | |||||||| |||||||| |||||||| || ||||| |||||||| ||||| |||||||||||||| ||||||    |||   |  |  | ||    ||   |  || |   |  | ||||  | |    |  || |||      |   ||||  ||||  |       |     
CCCAACATTAAGTGGAACGACGTTGCCGGCCTCGAGAGCGCCAAGCAGGCACTGCAGGAGGCCGTTATATTGCCCGTCAAGTTCCCGCAGTTCTTCACGGgtgagcgacggtacctaaaagcgttatcttttccccctttattaagctttgatcctga----taaaagtttggcgattgaaattgatatggggtcacaaaaggc---

upper sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G126860_T01 (Zea mays), 5'ss of exon 1
CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggtttttttacttttcggttaatcgattgaaggaagtgtgattttaaatatt-cgaaatttcaattgttcgattggaatggtttgtttttggttcag---
|||||||| |||||||||||||| || ||  | |||||||| ||||| || |||||||| || || || ||||| || ||||| || ||||||||||| ||||||       |||   ||   ||  ||  || |        |  |  ||||  || ||  |||  ||| |||         ||  ||| | | || ||     
CCCAACGTCAAGTGGAACGACGTTGCTGGCCTCGAGAGCGCCAAGCAAGCTCTGCAGGAGGCCGTCATATTGCCGGTCAAGTTCCCACAGTTCTTCACGGgtgagctacgggttatccttttttttttctttttattctttgatcctgataaaagtttcgtgattgtaatcgtt-----atggtgccttgctatggggtcgcaaa

upper sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 1
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 1
CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggtttttttacttttcggttaatcgattgaaggaagtgtgattttaaatattcgaaatttcaattgttcgattggaatggtttgtttttggttcag
|| ||  | ||||||   || || || ||| | || || || || || || ||||||||||| || || ||||| || |||||||| ||||||||||||||| |   ||| | || | |   | || || |||||||           ||   | |   || ||   |  | |  ||  |  || ||||||  |  ||   
CCTAATATCAAGTGGTCAGATGTTGCTGGGCTTGAAAGTGCTAAACAAGCTCTGCAGGAAGCTGTGATTTTGCCTGTCAAGTTTCCACAGTTCTTCACTGgtaa--atttgtgtaatctggagctattc-attgaagttttgaaaccgttctctttgtaaagttgtga--gctttatctgt-tgttttgttacttcttag-

upper sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 1
lower sequence: EDP06645 (Chlamydomonas reinhardtii), 5'ss of exon 4
CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgag-ggtttttttactttt--cggttaatcgattgaaggaagtgtgattttaaatattcgaaatttcaatt--gttcgattggaatggtttgtttttggttcag----------------------------------------------------
            ||| ||||||| || ||||| ||| |||| ||| |||| ||| |||| || || |||||||| || ||||| |||||||||||||| ||| || || ||    ||  |   | |   || | |    |      ||  ||       ||    |  |   |  |   |   ||  ||    |    |    |||                                                    
------------TGGGACGACGTGGCCGGGTTGGAGGGCGCCAAGGAGGCTCTGAAGGAGGCAGTGATCTTGCCAGTCAAGTTCCCGCAGTTCTTCACGGgtaagcggattgacgaccatgaacagaagatagttctgcgagtacttgccttgcgtggctcagcttccctgctaagggtgcacggggtgcagggcaactaaggcagaagataagcgcacgcggtgcagaacatggtggtgcggcttgtgtgtgcacag

upper sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S76_197V6.1 (Physcomitrella patens), 5'ss of exon 1
CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgt------gagggtttttttacttttcggttaatcgattgaaggaagtgtgattttaaatattcgaaatttcaattgttcgattggaatggtttgtttttggttcag
|| || ||   ||||   || || || ||  | || || || ||||||||| ||||||| || || |||||||||||||||||||| || || ||||| |||      || |   | | | |  || |     |    |   || ||||    |  | |  ||       |   |  |||   |   ||   |  || ||||     
CCAAATGTTCGGTGGGCTGATGTTGCTGGACTTGAAAGTGCCAAGCAGGCGTTGCAGGAGGCAGTGATCTTGCCCGTGAAGTTTCCCCAATTTTTCACAGgtttggaagaagagctctctgcggtttgaccgttatgatactgggagtggttctggagaggttaatggacttgttccttctgctc--atctatgattgttgg-----

upper sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S200_72V6.1 (Physcomitrella patens), 5'ss of exon 1
CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggtttttttacttttcggttaatcgattgaaggaagtgtgattttaaatattcgaaatttcaattgttcgattggaatg-gtttgtttttggttcag
|| || ||   ||||  ||| || || ||  | || ||||||||||||||| |||| || ||||| || |||||||| |||||||| || || ||||| |||  || |       |||| |   | |     ||  |  |   |  |||||  |  |  |      | || |  |     | ||   |    | |  | |  
CCAAATGTTCGGTGGGCCGATGTAGCTGGTCTCGAAAGCGCGAAGCAGGCGTTGCAAGAGGCGGTGATTTTGCCCGTCAAGTTTCCTCAATTTTTCACAGgtttggatgcggagcctttccaactgaatatctgttgcgacgttacttttatcttgttaacgaaagagttttgaggaaatagtgtactccactctactgc--

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|193486744|gb|FK448379.1|FK448379
EST:     GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTG                         GTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
genomic: GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggttt ... tttggttcagGTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
EST: gi|254343324|gb|GR857028.1|GR857028
EST:     GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTG                         GTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
genomic: GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggttt ... tttggttcagGTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
EST: gi|193707983|gb|FK642403.1|FK642403
EST:     GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTG                         GTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
genomic: GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggttt ... tttggttcagGTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
EST: gi|6482719|gb|AW201948.1|AW201948
EST:     GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTG                         GTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
genomic: GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggttt ... tttggttcagGTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
EST: gi|22522065|gb|BU080876.1|BU080876
EST:     GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTG                         GTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
genomic: GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggttt ... tttggttcagGTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
EST: gi|208318846|gb|GE111537.1|GE111537
EST:     GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTG                         GTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
genomic: GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggttt ... tttggttcagGTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
EST: gi|193456283|gb|FK423953.1|FK423953
EST:     GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTG                         GTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTGCGGACCGCCGGGGACGG
genomic: GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggttt ... tttggttcagGTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
EST: gi|15815934|gb|BI788209.1|BI788209
EST:     GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTG                         GTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG
genomic: GCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggttt ... tttggttcagGTAAGCGACGACCTTGGAGAGCGTTCTTGTTGTACGGACCGCCGGGGACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAACGTGAAGTGGAACGACGTCGCGGGGTTAGAGAGCGCGAAGCAGGCGCTGCAGGAAGCGGTTATCTTGCCCGTGAAGTTTCCGCAGTTCTTCACTGgtgagggtttttttacttttcggttaatcgattgaaggaagtgtgattttaaatattcgaaatttcaattgttcgattggaatggtttgtttttggttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG