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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccagtctcgacattttattagacaattacacatactagattttttgttcatcaattaatagtgaggttatggatctctgctttatag

Basic information

species Glycine max
transcript GLYMA11G34840.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 5
GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccagtctcgacattttattagacaattacacatactagattttttgttcatcaattaatagtgaggttatggatctctgctttatag
|| ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| || || |||  ||   || |   || | ||| ||||      |   |||     |  ||  |  |  ||  ||  | |    |                     
GTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCGgtttgtcaaacttc-atattgtatttcttt-tggtacaagtaggccttgatactattc--ttgtttgaacag---------------------

upper sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 6
GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccagtctcgacattttattagacaattacacatactagattttttgttcatcaattaatagtgaggttatggatctctgctttatag
|| ||||| ||||| || || ||||| ||||| || ||||||||||||||||||||||||||||| || || |||  ||  |   |   |    | || || |  || ||             ||||  |||      |||   |||  || |   | | ||        
GTGGCTGACTCACTTGAAAAGGGAACAGAACACGAGGATGAATACATGATCAGTGAAAAGGAGCTTCTTGTTAACCGgtt-tgtgaacttgtgtacttcataaagcactt------------cttttccttccaagtctaaatttgatattctttctatttggacag---

upper sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccagtctcgacattttat-tagacaattacacatactagattttttgttcatcaattaatagtgaggttatggatctctgctttatag
|||||||||||||| || |||||||| |||||||||||||| ||||||||||||||||||||||| || || |||| ||   | | |   |  |  |||   || ||| |   | ||| |  | ||||| |      |  || | |||  | |   || |     |  |||
GTTGCTGATTCACTTGAAAAAGGAACAGAACATGAAGATGAGTACATGATCAGTGAAAAGGAGCTTCTTGTTAACAGgtttatactgctccagctctttccataaacactctgagataatgtaatttttttaaggtcaagaaaactga--taacaaatgtgaaagt-gtag

upper sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 5
GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaa---ttccagtctcgac----attt-tatta-gacaattacacata-ctagattttttgttcat--caattaatagtgaggttatggatctctgctttatag
|| ||||| ||||| |||||||| ||||| || ||||||||||||||||||||||| || |||||||| || || | ||||   || || | | | |    ||||  |||| | |  |||||  || ||||  || |  || ||   ||||   ||| |        ||   || |||  ||
GTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAGgtaaagatttcattattgtctactatttacattatgcctgttacaactagctaggattgtattttatggtaattcccagtcaatacgcctattcttggtttgcag

upper sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S303_47V6.1 (Physcomitrella patens), 5'ss of exon 5
GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgta-attccagtctcgacattttattagacaattacacatac-tagattttttgttcatcaattaatagtgaggttatggatctctgctt-tatag----
|| || |||||  | || || || || |||||||||||||| |||||||||||||| |||||||| || || |||| |||  |      ||       ||  ||| |    |     |  |  |   ||  | | ||||||  |  || | | | | | |   |    |  ||    
GTGGCAGATTCTTTAGAAAAGGGCACGGAACATGAAGATGAGTACATGATCAGTGAGAAGGAGCTTCTTGTTAACAGgtatgtctttccctttttcccttgataggctgggatgtcgatgtttagaattgatgcctcaatttgttttgcgttaaggaaacgaagtgaatgcagattt

upper sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S266_44V6.1 (Physcomitrella patens), 5'ss of exon 3
GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccagtctcgacattttattagacaattacacatactagattt---tttgttcatcaattaatagtgaggttatggatc--tctgctttatag----
||||| |||||  | ||||| || || |||||||||||||||||||||||||| || ||||| || || |||||||||| | ||   ||||| | || |  |  |      |   |   | |        ||   |||  ||   | |||||   |   ||  | ||  |  | |    
GTTGCGGATTCTTTAGAGAAGGGTACGGAACATGAAGATGAATACATGATCAGCGAGAAGGAACTGCTTGTAAACAAgttagtctt-tctcgtctttctcgtctatctcctcttctttgaaagagaggcatgccgatcg-ttgcgattgaggccttaagtcgttttgaatatttgaagc

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|254320117|gb|GR831033.1|GR831033
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|151411948|gb|EV281759.1|EV281759
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|151396616|gb|EV266493.1|EV266493
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|151410774|gb|EV280589.1|EV280589
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|192320522|gb|FK011932.1|FK011932
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|207701893|gb|GD683445.1|GD683445
EST:     AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAAACAA                         ATTCATTTCTATCCCAAAGGACATGGG
genomic: AACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAA-CAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGG
EST: gi|298191865|gb|HO035947.1|HO035947
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|208256579|gb|GE057408.1|GE057408
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGA
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGA
EST: gi|13477866|gb|BG507568.1|BG507568
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|151405191|gb|EV275005.1|EV275005
EST:     GAACATGAGGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|208221539|gb|GE018619.1|GE018619
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTTTATCCCAAAGGACA
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACA
EST: gi|208098926|gb|GD891497.1|GD891497
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGT-AACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|8286428|gb|BE023996.1|BE023996
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|193563080|gb|FK519513.1|FK519513
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|192320523|gb|FK011933.1|FK011933
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|151412057|gb|EV281869.1|EV281869
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|42723157|gb|CK769056.1|CK769056
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|193492237|gb|FK455263.1|FK455263
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACA
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACA
EST: gi|9987096|gb|BE661204.1|BE661204
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGT
EST: gi|208134214|gb|GD927919.1|GD927919
EST:     GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA                         ATTCATTTCTATCCCAAAGGA
genomic: GAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccag ... tgctttatagATTCATTTCTATCCCAAAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAAgtaattccagtctcgacattttattagacaattacacatactagattttttgttcatcaattaatagtgaggttatggatctctgctttatag

- - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC