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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattttaatttctcttgcagtgtatattcattaattgtgtggttggccccattatttctattctctaacacctgattaatcattcccttaatttg...

Basic information

species Glycine max
transcript GLYMA12G01680.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01680.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g47310.1 (Oryza sativa), 5'ss of exon 3
CTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAA-----GCTAAGgtttcaattttaatttctcttgcagtgtatattcattaattgtgtggttggccccattatttctattctctaacacctgattaatcattcccttaatttg
|||| | |||| ||| ||  |  |||| || || || |||||| | |||||||| || ||||||||||||||||| ||||| ||||| ||||||     | |||| |     | ||  ||   ||| |||   | |   |  ||| |     |     || |   ||  |   | ||| || |  |  | |||| ||    |   
CTTTCAAGTTGGTGATGCATTGGAGCAGCCTTTTCCTGATGGGCAGTTTGATCTTGTCTGGTCCATGGAGAGTGGCGAGCACATGCCAGACAAACGGCAGgtaagatactcctcttttttatccttacagaaaaaaagaa--aatgggaaaatgtaatccctccgtttcaggttataagactt--tctagcattgccacgttca-

upper sequence: GLYMA12G01680.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G035213_T01 (Zea mays), 5'ss of exon 3
CTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtt-tcaattttaat--ttctcttgcagtgtatattcattaattgtgtggttggccccattatttctattctctaacacctgattaatcattcccttaatttg
  |  | |||||||| |||||  ||||||| || || || ||| | || |||||||||||||||||||||||||| ||||| ||||| |||||    |||||   |  || || |  | || ||    || |     |   |  ||    || |    |  |     |   |||   | | ||| |   |    |   |    
TCTGCAAGTTGCTGATGCTCTGGAGCAACCGTTTCCTGACGGGCAGTTCGATCTGGTGTGGTCCATGGAGAGTGGCGAGCACATGCCGGACAAGAGAAAGgtaacctgttctattcgtcctttttttttgaaagacaaggcagcgtagctttcgagaaaaaagaatcaagatctggaatcagatgatgtaagggcactac---

upper sequence: GLYMA12G01680.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0039g01410.t01 (Vitis vinifera), 5'ss of exon 3
CTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtt--tcaattttaatttctcttgcagtgtatattcattaattgtgtggttggccccattatttctattctct-----aacacct--gattaatcattcccttaatttg---------------------------------------------------------
 ||  | ||||| || |||||  | ||||| || || |||||  ||||||||||||| |||||||||||||||||||| || ||||||||||||   |||||   |   | | | |||| ||  ||   | | |   || ||  | |       ||    ||||  ||||  |     || ||||  | |||||  |    ||| | |                                                          
TTTCCAAGTTGCAGATGCTCTGGATCAACCGTTTCCTGATGGACAATTTGATCTGGTTTGGTCCATGGAGAGTGGAGAACACATGCCTGACAAAAAAAAGgtggattcttctcactttcactctcacactttgtattttgatcatattac-attccttggattttgattcattgaacaaatacctatgcttaattttcatgttattgtattggttgctgtggatgttgacttatgttattctacttgattttgttggctttgtcag

upper sequence: GLYMA12G01680.1 (Glycine max), 5'ss of exon 3
lower sequence: EDP02465 (Chlamydomonas reinhardtii), 5'ss of exon 7
CTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattttaatttctcttgcagtgtatattcattaattgtgtggttggccccattatttctattctctaacacctgattaatcattcccttaatttg------------
       || |  ||||| ||   ||| || |||  ||  ||    || || |||||||||||||||||||| || ||||| ||||| |||||      || | ||     |      |  |  | ||   |     |   | | ||  || ||   |      ||     |||  |  |  |  ||  | |  ||  |             
-------GTGGGCGACGCGCTGGCGCAGCCGTTCGAGGCCGGCGCCTTCGACCTGGTGTGGTCCATGGAGAGCGGCGAGCACATGCCCGACAAGAA-

upper sequence: GLYMA12G01680.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S31_53V6.2 (Physcomitrella patens), 5'ss of exon 2
CTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgttt-caattttaatttctcttgcagtgtatattcattaattgtgtggttggccccat-tatttctat-tctctaacacctgattaatcattcccttaatttg---------------------------------------------------------------------
 ||  |||| ||  | || || || || || || | ||||||    |||||||| ||||||||||||||||| || ||||| ||||| |||||    ||||||    |  |||        ||     || ||| | | ||| |  | ||      || ||| | ||| | | ||  | ||  ||     ||  || || ||                                                                      
TTTCCAGGTAGCGAATGCCCTGAACCAGCCCTTTCAGGATGGTTCGTTTGATCTCGTGTGGTCCATGGAGAGCGGCGAGCACATGCCAGACAAGAAAAAGgttagtgacattagggataaatgtta-atacattgacttattcttggtttatatatatatatatatatatatatacaatctttttgcgttttttctgaaattcatgtagttcaatgtaaagtctggatgcattcgctaagtttgggttctttctctgtgaatggctttgaag

upper sequence: GLYMA12G01680.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ23345 (Selaginella moellendorffii), 5'ss of exon 3
CTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattttaatttctcttgcagtgtatattcattaattgtgtggttggccccattatttctattctctaacacctgattaatcattcccttaatttg
 ||| | || || || ||| | |  || || || || ||     |||||||||| |||||||| |||||||| || ||||||||||| |||||    || ||   ||  |  ||||     | | || |   || | |    ||      |   | ||  ||                                      
GTTTCAAGTCGCGGATGCTTTGATCCAGCCGTTTCCAGACAACGAATTTGATCTCGTGTGGTCGATGGAGAGCGGGGAGCATATGCCAGACAAGCGGAAAgt---aagctccatttg----gtactggaagctcctcag--atgctaacagtagcgtttcttag------------------------------------

upper sequence: GLYMA12G01680.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ25322 (Selaginella moellendorffii), 5'ss of exon 3
CTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattttaatttctcttgcagtgtatattcattaattgtgtggttggccccattatttctattctctaacacctgattaatcattcccttaatttg
 ||| | || || || ||| | || || || || || ||     |||||||||| |||||||| |||||||| || ||||||||||| |||||    || ||   ||  |  ||||     | | || |   || | |    ||  |   |   | ||  ||                                      
GTTTCAAGTCGCGGATGCTTTGAACCAGCCGTTTCCAGACAACGAATTTGATCTCGTGTGGTCGATGGAGAGCGGGGAGCATATGCCAGACAAGCGGAAAgt---aagctccatttg----gtactggaagctcctcag--atgctgacagtagcgttccttag------------------------------------

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|120531233|gb|EH259366.1|EH259366
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattt ... caaccgacagTTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|213602117|gb|DB962610.1|DB962610
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattt ... caaccgacagTTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|151406224|gb|EV276039.1|EV276039
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattt ... caaccgacagTTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|58023365|gb|CX710106.1|CX710106
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattt ... caaccgacagTTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|57575258|gb|CX548233.1|CX548233
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattt ... caaccgacagTTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|14125812|gb|BG790250.1|BG790250
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattt ... caaccgacagTTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|13482030|gb|BG511373.1|BG511373
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGCGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattt ... caaccgacagTTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
EST: gi|26056288|gb|CA799202.1|CA799202
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAATTA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattt ... caaccgacagTTTGTTGGAGAATTA
EST: gi|192319801|gb|FK013801.1|FK013801
EST:     ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAG                         TTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA
genomic: ATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattt ... caaccgacagTTTGTTGGAGAATTAGCTCGGGTAGCAGCACCAGGTGCCACTATAATAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGAGGTTGCTGACGCTCTAAAGCAACCATTCCCGGATGGGAAATTTGATCTGGTGTGGTCCATGGAGAGTGGAGAGCATATGCCTGACAAAGCTAAGgtttcaattttaatttctcttgcagtgtatattcattaattgtgtggttggccccattatttctattctctaacacctgattaatcattcccttaatttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA