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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATACCCCACAGGGCGCCTGATCTTCCTGCTAAGTTCAAATCCATGCTTGTCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccagcttattgaaataattatttctgattcagttttgactgttgtcatgctgcattggaatataatcagttgtctctactttatagttttcaac...

Basic information

species Glycine max
transcript GLYMA02G43610.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G43610.3 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os02g16550.1 (Oryza sativa), 5'ss of exon 1
CATACCCCACAGGGCGCCTGATCTTCCTGCTAAGTTCAAATCCATGCTTGTCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtc-cagcttattgaaataattatttctgattcagttttgactgttgtcatgctgcattggaatataatcagttgtctctactttatagttttcaac--
| | || ||| ||||| | || || || || |||||||| |||||||| ||||| ||||||||||||||||| || || || || ||  | || || || ||  |   | |||        |   ||   | | |||  |  ||  ||  | |  ||  |||     |  | |   |||| | ||   |   ||||   |   
CGTGCCGCACCGGGCGGCCGACCTGCCGGCCAAGTTCAAGTCCATGCTCGTCCCGGGCAAGATCCAGCACATCATCTGCACGGGGAACCTCTGCATCAAGgttagcggccgctaccccccttccctaccgcggtttc--tcgtgcttggcg-cgcgccccatcatggttgactagtttgtttgtagcgtcctgtttagcattg

upper sequence: GLYMA02G43610.3 (Glycine max), 5'ss of exon 3
lower sequence: AT3G47810.3 (Arabidopsis thaliana), 5'ss of exon 2
CATACCCCACAGGGCGCCTGATCTTCCTGCTAAGTTCAAATCCATGCTTGTCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgta-tgtccagctta-ttgaaataattatttctgat-tcagttttgactgttgtcatgctgcattggaat-ataatcagttgtctctactttatagttttcaac
  ||||||| || ||| ||||||| ||| ||||||||||||| |||||||| ||||| ||||| || ||||| || || ||||||||| | || || |||||| |||     ||  || ||||  | |  | | |  ||  |  |     || |  |  | | ||    |  |  |  | |   |||   | ||     |    
TGTACCCCATAGAGCGGCTGATCTACCTCCTAAGTTCAAATCAATGCTTGTTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgttttttttccttcaaattttcaacttttacatctctagtatgctttattttttttcgttaatgtcgttgtgggatcattctgtctgatgtaact----

upper sequence: GLYMA02G43610.3 (Glycine max), 5'ss of exon 3
lower sequence: Vv17s0000g05880.t01 (Vitis vinifera), 5'ss of exon 1
CATACCCCACAGGGCGCCTGATCTTCCTGCTAAGTTCAAATCCATGCTTGTCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccagcttattgaaataattatttctgattcagttttgactgttgtcatgctg--cattggaatataatcagttgtctctactttatagttttcaac---
 || ||  | ||||| |||||| | ||  | |||||||||||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| ||||| |||||  ||   |||| ||    |   | ||  |  |||| | ||  ||||||  ||||     |||  ||||  ||   | | ||    |||||             
TATCCCTGATAGGGCTCCTGATTTGCCGCCAAAGTTCAAATCCATGCTTGTTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagt---gctttttcttctttcttttcttctttcattctt--ctgttgctatgccagttatttaaatactatttctggacttgggtttatgagcaaatgtagg

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|4286973|gb|AI441123.1|AI441123
EST:     TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAA                         GAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
genomic: TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccag ... tcatcttcagGAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
EST: gi|213587294|gb|DB955502.1|DB955502
EST:     TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAA                         GAAATTCATGACTACTTAAAGACTCTTTGT
genomic: TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccag ... tcatcttcagGAAATTCATGACTACTTAAAGACTCTTTGT
EST: gi|151402170|gb|EV271983.1|EV271983
EST:     TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAA                         GAAATTCATGACTACTTAAAGACTCTTTCGTCCAGACTTGCATATAACTCG
genomic: TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccag ... tcatcttcagGAAATTCATGACTACTTAAAGACTCTTT-GTCCAGACTTGCATATAACTCG
EST: gi|15285030|gb|BI468921.1|BI468921
EST:     TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAA                         GAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
genomic: TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccag ... tcatcttcagGAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
EST: gi|298163806|gb|HO012539.1|HO012539
EST:     TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAA                         GAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
genomic: TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccag ... tcatcttcagGAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
EST: gi|298195454|gb|HO043845.1|HO043845
EST:     TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAA                         GAAATCCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
genomic: TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccag ... tcatcttcagGAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
EST: gi|192331560|gb|FK019949.1|FK019949
EST:     TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAA                         GAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
genomic: TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccag ... tcatcttcagGAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
EST: gi|23057396|gb|BU578070.1|BU578070
EST:     TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAA                         GAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT
genomic: TCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccag ... tcatcttcagGAAATTCATGACTACTTAAAGACTCTTTGTCCAGACTTGCATATAACTCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATACCCCACAGGGCGCCTGATCTTCCTGCTAAGTTCAAATCCATGCTTGTCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgtatgtccagcttattgaaataattatttctgattcagttttgactgttgtcatgctgcattggaatataatcagttgtctctactttatagttttcaac

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