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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacatagtattttctaaatacttaggaaaacgttttttttagtttatttatttaaaatatttgaagatgattcaattgcaacactgtaataaaata...

Basic information

species Glycine max
transcript GLYMA13G06840.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G06840.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os11g41140.1 (Oryza sativa), 5'ss of exon 4
AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgta-ctacatagtattttctaaatacttaggaaaacgttttttttagtttatttatttaaaatatttgaagatgattcaattgcaacactgtaataaaata
 |||||||| | |||| | |   | ||||| |||||||| |||||||| || ||||||||||||||||| ||||||||    || ||||| ||||||||||||  |      ||  |  |   |  ||          |  |||| ||  | |||| |    | || ||  ||| ||   ||       |   |   |  |
TGAGAATCCTAGGATAGTAATGCAGTGCTCACATCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGTTTGTGGAAAGgtaattttgctttagctcttccttttttttcctccttataatttttgtccagttatatgctttgtt-gactatgtttgctttttctaggtactacgtacaa

upper sequence: GLYMA13G06840.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G468260_T04 (Zea mays), 5'ss of exon 1
AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacatagtattttctaaatact-taggaaaacgttttttttagtttatttatttaaaatatttgaagatgattcaattgca-acactgtaataaaata
 |||||||| | |||| | |   | ||||| || ||||| |||||||| || ||||||||||||||||| ||||||||    || |||||||||||||||||| |   |     | | |   |||  |   ||    || ||  |     |  ||| | ||       |  |   ||   |  |     ||   || ||   
TGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGTCTGTGGAAAGgtaatttgtttatctctttgcttacccttataatttattattgctgtcacacatatgtgaagcccgacacaaaatttatgtcacctgttctacgatgaag--

upper sequence: GLYMA13G06840.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G02290.2 (Arabidopsis thaliana), 5'ss of exon 3
AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacatagtattttctaaatacttaggaaaacgttttttttagttt---atttatttaaaatatttgaagatgattcaa-ttgcaacactgtaataaaata
|||||| ||||||||  |||||||||| || || ||||| |||||| ||||||||||||||||||||||||||||||| |||||||| ||||| |||||||||     |  | ||||||  || ||||| |  | ||   | | |   |    |  |   ||||      | | |  |  || |||||        || |    
AGAGAACCCAAAGATTGTGACAAAATGTTCACACCATTTCCACCTTAGTTGCATTTATGAGTGGATGGAGAGAAGTGAAAACTGTCCAGTCTGCGGAAAGgtaaccactttttttttctgcattcttagaacgaagtgcgtataaaactcccgtcaaagcaaaaggccatatgcttttcgaaattgcacggtctagatga----

upper sequence: GLYMA13G06840.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G38895.1 (Arabidopsis thaliana), 5'ss of exon 4
AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacatagtattttctaaatacttaggaaaacgttttttttagtttatttatttaaaatatttgaa-gatgattcaattgcaacact--gtaataaaata
 |||||||| |||||||| || || || ||||| ||||| |||||| | || |||||||| ||||||||||||||||| |  || || |||||||||||||||   | | |  || |  ||| ||||   ||  ||  |||  | |  | ||   | ||  |  || |  |||  |  || |||| || |  ||| || ||  
GGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGTCTGTGGAAAGgtaactcgtcgctttctacaaa-actttaaaacccggatttggtcgaatgttccatcaatctccttcatcgatattaaaagtgcatcattttgtattagaa--

upper sequence: GLYMA13G06840.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G15790.2 (Arabidopsis thaliana), 5'ss of exon 4
AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacatagtattttctaaatacttaggaaaacgttttttttagtttatttatttaaaatatttgaagatgattcaattgcaa-cac-tgtaataaaata-----
|||||| || |||||  | ||||| || ||||| ||||| |||||  ||||||||||||| ||||||||||||||||| ||||| ||||| ||||||||||||      |  | |||  |  | |||   |    |||||       | ||||| | |   | |  ||    || |||    | | |||  ||||  | |       
AGAGAACCCGAAGATTGTTACAAAGTGTTCTCACCATTTCCACCTCAGTTGCATTTATGAATGGATGGAGAGAAGTGAAAACTGCCCTGTTTGTGGAAAGgta------aacacttttcatgttcttccaagccagttttcggcttctcatttact-agtgtttcagagtcagactcagacaccatcacgcgtaaatagacgagtga

upper sequence: GLYMA13G06840.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv14s0083g01000.t01 (Vitis vinifera), 5'ss of exon 4
AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacatagtattttctaaatacttaggaaaacgttttttttagtttatttatttaaaatatttgaagatgattcaattgcaacactgta-ataaaata
||| ||||| ||||||||||||||||||||||| ||||||||||||||||| || ||||| ||||||||||||||||| |  ||||| |||||||| ||||||     |   ||||     ||    ||      ||||  |||    ||    |    |    | |   |    |  | | ||   ||  | ||||||| 
AGAAAATCCCAAGATAATGACAAAATGCTCTCACCATTTTCACCTTGGTTGTATATATGAATGGATGGAGAGAAGTGAAACATGTCCAGTCTGTGGCAAGgtatcgtttttcatttctgtcatgtgaagttgcttgtttactttgtcatagcattgattaggcataggtcacatcttcaatacactgcttcatataaaat-

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|192304212|gb|FG996394.1|FG996394
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAG-TCTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
EST: gi|37997745|gb|CF809334.1|CF809334
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
EST: gi|192304187|gb|FG996383.1|FG996383
EST:     GCATTTATGGGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
EST: gi|8826638|gb|BE210368.1|BE210368
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAGCTGTCCTGTCTGTGGAAAG                         GTGATGGTGTTCGATGGAACGACTTTCAC
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCAC
EST: gi|9985548|gb|BE659656.1|BE659656
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
EST: gi|57575660|gb|CX548635.1|CX548635
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
EST: gi|58015626|gb|CX702368.1|CX702368
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
EST: gi|192304213|gb|FG996395.1|FG996395
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTTTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
EST: gi|192300484|gb|FG987911.1|FG987911
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
EST: gi|192299720|gb|FG993300.1|FG993300
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTTTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
EST: gi|58015294|gb|CX702036.1|CX702036
EST:     GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAG                         GTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT
genomic: GCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacata ... tctgatctagGTGATGGTATTCGATGAAACGACTTTCACTTGATTACAAGGTCTGTGTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCTGTCTGTGGAAAGgtactacatagtattttctaaatacttaggaaaacgttttttttagtttatttatttaaaatatttgaagatgattcaattgcaacactgtaataaaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT