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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttgatactaatttacttgctgtctgatattatacaccttgttttcctcaatgttattgtttattttcatctgtgacagtgtgaaattttcctat...

Basic information

species Glycine max
transcript GLYMA07G07270.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G07270.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 5'ss of exon 2
AGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttgatactaatttacttgctgtctgatatta-tacaccttgttttcctcaatgttattgtttattttcatctg--tgacagtgtgaaattttcctat
||||||||| |||||||||||||||||||| || |||   || ||||||||  ||||  |  ||||||| || || ||||| |||||||| || |  ||||||||     |  |  || | ||| | |  || |||  ||    || ||   |  | |     |    | | | |  |   | |  | |||  |||| | |  
AGTTGCCATCAAGAAGATTGGCAATGCATTCGACAACCATATCGATGCCAAGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAATgtaagagctgt-ttgtttaaattggttttcgacattcctagtgattattgatcgaacttggccttaccactattaggtaatttattgggtgtgatttacat--

upper sequence: GLYMA07G07270.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G46070.2 (Arabidopsis thaliana), 5'ss of exon 2
AGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttgatactaatttacttgctgtctgatattatacaccttgttttcctcaatgttattgtttattttca---tctgtga----cagtgtgaaattttcct-at------------------------------------------------
||| || ||||||||||| || ||||| ||||||||||  || ||||| || || ||  |||| ||||||||||||||  |||| ||||||||||  || |||||  | |  |    || ||  |  | ||| |  | |    ||   || |||||  ||  |   | | |  |   |   |||    ||| || ||||  || | ||                                                
AGTGGCTATTAAGAAGATCGGTAATGCTTTTGATAACATCATCGATGCTAAGAGAACGCTACGTGAAATTAAACTTCTCAGGCATATGGATCATGAGAACgtaagccttaagcatcatttctcac-atttgaca--acatcttttaagtttctcaaatttgctagatctatcaagtgttcctgatcttcagggtcaaatgctctttatatataatttcgtttactctaatcttcaagcctcggtttgattctttag

upper sequence: GLYMA07G07270.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 5'ss of exon 2
AGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagttt-gatactaatttacttgctgtctgatattatacaccttgttttcctcaatgttattgtttattttcatctgtgacagtgtga-aattttcctat
||||||||||||||||||||| |||||||||||||| || |||||||||||| |||| ||||| |||||||| |||||||| ||||||||||||| |||||||||||| | | |     ||| |   | |   ||||       | ||||| ||   | |  |||   |  |   | |||     | | | |||| |  |  
AGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATTAAGCTTCTTCGCCACATGGATCATGAAAATgtaagttttggttcctccatacctcgggccaattattgcttctatagttttactgtctttgtttggcaagatgattgtgttttgctctaataattgtttt--

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|11275203|gb|BF325526.1|BF325526
EST:     AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAAT                         ATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
genomic: AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttga ... tccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
EST: gi|151396148|gb|EV266025.1|EV266025
EST:     AAAGGACCTTACGAGAAATTAGACTTCTTCGGCACATGGAACATGCAAAT                         ATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
genomic: AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttga ... tccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
EST: gi|16996008|gb|BM085380.1|BM085380
EST:     AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAAT                         ATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
genomic: AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttga ... tccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
EST: gi|254328119|gb|GR835084.1|GR835084
EST:     AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAAT                         ATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
genomic: AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttga ... tccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
EST: gi|22522756|gb|BU081567.1|BU081567
EST:     AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAAT                         ATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
genomic: AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttga ... tccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
EST: gi|254315198|gb|GR830191.1|GR830191
EST:     AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAAT                         ATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
genomic: AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttga ... tccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
EST: gi|5127030|gb|AI748766.1|AI748766
EST:     GAAATTAAACTTCTTCGGCACATGGATCATGCAAAT                         ATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
genomic: GAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttga ... tccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAAT
EST: gi|9264552|gb|BE352699.1|BE352699
EST:     AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAAT                         ATTATGTCCATTAAAGATATTATACCGTCCTCCACAGAAGGAAAACTTCAA
genomic: AAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttga ... tccaatgcagATTATGTCCATTAAAGATATTATAC-GTCCTCCACAGAAGGAAAACTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATTAAACTTCTTCGGCACATGGATCATGCAAATgtaagtttgatactaatttacttgctgtctgatattatacaccttgttttcctcaatgttattgtttattttcatctgtgacagtgtgaaattttcctat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA