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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTCACTGATAGCATGCAAAAGCTACTTATTGTTATGCAAAGACTGGATGAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAGgtaagttcaatggataggacttttgattcagaagctccctaatcgtacttgatctgtacttagtttattgacttctgccacatggctaaatatgtgaacc...

Basic information

species Glycine max
transcript GLYMA17G04580.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os01g14810.1 (Oryza sativa), 5'ss of exon 14
ACCTCACTGATAGCATGCAAAAGCTACTTATTGTTATGCAAAGACTGGATGAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAGgtaagttcaatggataggacttttg--attcagaagctccctaatcgtacttgatctgtacttagtttattgacttctgccacatggctaaatatgtgaacc
| || || || || ||||||||| | || ||||||||||| ||| | ||||| |||||||| |||||||| ||  ||||||| ||||| ||||||  |||||||           ||   ||  |  ||||   |  ||  | |  | |   ||   ||    | ||  | |  |   |     | ||   || | |     
AGCTTACAGAAAGTATGCAAAAGTTGCTCATTGTTATGCAGAGATTAGATGAAAAAATTGCACCAATGCTAGAATCAGATGGAGAGCTGTTCAATAAAAGgtaaagcaggcatgcagtcattgcgtaattcctcatgtctttgaatgcaa--gaaacgtctgaaattcgtcgcttctagatctgttgccctatgtatttttg

upper sequence: GLYMA17G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os01g14810.3 (Oryza sativa), 5'ss of exon 14
ACCTCACTGATAGCATGCAAAAGCTACTTATTGTTATGCAAAGACTGGATGAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAGgtaagttcaatggataggactt--ttgattcagaagctccctaatcgtacttgatctgtacttagtttattgacttctgccacatggctaaatatgtgaacc---
| || || || || ||||||||| | || ||||||||||| ||| | ||||| |||||||| |||||||| ||  ||||||| ||||| ||||||  |||||||           ||   ||   | ||||   |  ||  | |  | |   ||   ||    | ||  | |  |   |     | ||   || | |        
AGCTTACAGAAAGTATGCAAAAGTTGCTCATTGTTATGCAGAGATTAGATGAAAAAATTGCACCAATGCTAGAATCAGATGGAGAGCTGTTCAATAAAAGgtaaagcaggcatgcagtcattgcgtaattcctcatgtctttgaatgcaa--gaaacgtctgaaattcgtcgcttctagatctgttgccctatgtatttttgcag

upper sequence: GLYMA17G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: AT5G48960.1 (Arabidopsis thaliana), 5'ss of exon 14
ACCTCACTGATAGCATGCAAAAGCTACTTATTGTTATGCAAAGACTGGATGAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAGgtaagttcaatggataggacttttgattcagaagctccctaatcgtacttgatctgtacttagtttattgacttctgccacatggctaaatatgtgaacc
| || || || | |||||||||||| |||||||| ||||||||||| ||||| || |||| || |||||||||  ||||||| |||||||| ||   |||||||    ||        ||   ||    |  |      || ||    || |     |   |  |   |||    |    | |||     | ||      
AACTGACAGAGACCATGCAAAAGCTTCTTATTGTAATGCAAAGACTAGATGACAAGATTGGTCTAATGCTGGAAACAGATGGCGAGCTCTTTAACAAAAGgtaaaaagaaaaagacaaacaaatgtagtaaga-----ttactcaagattcacagaaagggatatgtctgagccataattcttgggctgttttgcag---

upper sequence: GLYMA17G04580.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv05s0020g00880.t01 (Vitis vinifera), 5'ss of exon 14
ACCTCACTGATAGCATGCAAAAGCTACTTATTGTTATGCAAAGACTGGATGAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAGgtaagttcaa--tggat--aggacttttgattcagaagctccctaatcgtacttgatctgtacttagtttattgacttctgccacatggctaaatatgtgaacc
  |||||||| | |||||| ||||||||| |||||||||||||| | || || |||||||| |||||| | || || ||||| |||| ||| |    ||||||||   |   | | |  ||||      ||| |     |    |||    ||| | | || |||  || |||  ||| |||  ||    | | |   || |  
GACTCACTGAGACCATGCAGAAGCTACTTCTTGTTATGCAAAGATTAGACGAAAAAATTGCACCAATGTTAGATGCTGATGGAGAGCACTTTAGCAAAAGgtaagagaaggttagttgcaggaaaaaaaatttaatttgttgaaaatatctcttta-cagttcttttttaattttcttttgcagcaaaaatta-tccctgga--

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|51335476|gb|CO979342.1|CO979342
EST:     GAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAG                         GTGGGGTTTTCTATCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAG
genomic: GAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAGgtaagttcaa ... tctgcattagGTGGGGTTTTCTATCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAG
EST: gi|298169844|gb|HO018468.1|HO018468
EST:     GAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAG                         GTGGGGTTTTCTATCTCGTGCTGGGCTGTGGGATAAAAGCCACCTGATGAG
genomic: GAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAGgtaagttcaa ... tctgcattagGTGGGGTTTTCTATCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAG
EST: gi|58022071|gb|CX708812.1|CX708812
EST:     TTCAATTCAAG                         GTGGGGTTTTCTATCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAG
genomic: TTCAATTCAAGgtaagttcaa ... tctgcattagGTGGGGTTTTCTATCTCGTGCTGGGCTGTGGGATAAAAGCCACTTGATGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCTCACTGATAGCATGCAAAAGCTACTTATTGTTATGCAAAGACTGGATGAGAAAATTGCTCCAATGCTGGAGGCAGATGGGGAGCTCTTCAATTCAAGgtaagttcaatggataggacttttgattcagaagctccctaatcgtacttgatctgtacttagtttattgacttctgccacatggctaaatatgtgaacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT