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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaagcctgggaggtggacttgagtttgtgccatattgttatgtgtgtttgggtgataactcattgctgctttgctctggtcctggtgttgtttt...

Basic information

species Glycine max
transcript GLYMA05G22320.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 6
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 5'ss of exon 6
ATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagg-----gaagcctgggaggtggacttgagtttgtgccatattgttatgtgtgtttgggtgataactcattgctgctttgctctggtcctggtgttgtttt--
|||||||| |||||||| ||||||||||| ||||| |||||||||||| |||||||||| || |||||||        |||| |      ||          | ||      | |||  |   |    || ||| || |    | |  | || ||    |     | |     
ATATTCCGCAAGGAGCCGTTCTTTTATGGCCATGACAACTATGATCAATTGGTCAAAATTGCGAAGgtaacattacaaaagctttcatcatgtctcgtctcctctgaacagattttacattcctccaagttatagctaaa-aatacgattctatgtatttataactatggcag

upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 6
ATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaagcctgggaggtggacttgagtttgtgccatattgttatgtgtgtttgggtgataactcattg-ctgctttgctctggtcctggtgttgtttt-------
|| ||||| ||||||||||| || || || |||||||| |||||||||||||| |||||||||||||||||       ||  |  |     |  ||           | | | |    | ||  |   |||   ||   |   |   | ||    ||  ||  ||         
ATTTTCCGCAAGGAGCCATTTTTCTACGGGCATGATAATTATGATCAACTGGTTAAAATAGCTAAGgtaag-------tgttaaatttctctctgtcaactagtagatatcaggaacatctgaattccaacagcttaattatatcattttgaaagtga-gtctttgcagagagc

upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 7
ATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaag-ggaagcctgggaggt----ggacttgagtttgtgccatattgttat--gtgtgtttgggtgataactcattgctgctttgctctggtcctggtgttgtttt--------------------------------------
|| || || |||||||||||||||||||||||||| || |||||||| || || || || || |||||    ||||  ||            | ||| | |  ||  |   |  ||     | | | ||  |  |  |||  | |||  || |||  | ||  || |   | |                                      
ATCTTTCGGAAGGAGCCATTCTTTTATGGACATGACAATTATGATCAGCTTGTGAAGATTGCCAAGgtgctcggaaatctcatttactatcagccttcaatcagtcactgctcattcgtaatttttctgaatcgtttctc-ctcctgtgtttctcaaggccatgtttaaatcttcgttctaaatctaatctttgttgttacctgaaatcag

upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 7
ATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgta-agggaagcctgggaggtggacttgagtttgtgc-----catattgttatgtgtgt---ttgggtgataactcat--tgctgctttgctctggtcctggtgttgtttt-------------------------------
||||| || |||||||||||||||||||| ||||| || ||||||||||| || || || ||||||||  || |     |   |  | || |||  ||   ||      ||||   | | | | |   |||  | | || ||||  | |||  || | |    ||  ||  ||||||                               
ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAGgtgcagtggcagttcatacatagatttgccttcaagcagttatatatcactttttatttattttgtataaaaagtcatattactgtctttcgcaacgccaagttgtgttttgagccttatctttgtgggtgtctgataccag

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|37995826|gb|CF807415.1|CF807415
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|31470201|gb|CD412349.1|CD412349
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|15815566|gb|BI787841.1|BI787841
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|16279966|gb|BI943709.1|BI943709
EST:     TGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: TGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|18848708|gb|BM567820.1|BM567820
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|17153984|gb|BM143917.1|BM143917
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|20814462|gb|BQ298940.1|BQ298940
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|192303250|gb|FG995586.1|FG995586
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|31465610|gb|CD407638.1|CD407638
EST:     CATTCTTTTATGGACATGATAACTATGATTAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|16343159|gb|BI968754.1|BI968754
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|22927857|gb|BU544996.1|BU544996
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|4299430|gb|AI442903.1|AI442903
EST:     ATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: ATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|9819518|gb|BE555031.1|BE555031
EST:     CATTCCTTTATGGACATGATAACTATGATCAACTGCTCAAAATAGCTCAC                         GTTCTTTGGACTGACGGATTAAGTGCTTATTTA
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTA
EST: gi|7640075|gb|AW734384.1|AW734384
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
EST: gi|17401154|gb|BM177936.1|BM177936
EST:     CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAG                         GTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG
genomic: CATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaag ... catgcaatagGTACTTGGGACAGACGGATTAAGTGCATATTTAGATAAGTATCGAATAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATTCCGTAAGGAGCCATTCTTTTATGGACATGATAACTATGATCAACTGGTCAAAATAGCTAAGgtaagggaagcctgggaggtggacttgagtttgtgccatattgttatgtgtgtttgggtgataactcattgctgctttgctctggtcctggtgttgtttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgggtg