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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTATGGTGCAACAAGCTATGCAATATATTGATGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgctatgtttgaactttttgtttgttttatagcttttcattatgtgattatgtatgatttatatgtttttatcatttattag

Basic information

species Glycine max
transcript GLYMA05G32030.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 3
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 5'ss of exon 3
AGCTATGGTGCAACAAGCTATGCAATATATTGATGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgctatgtttgaactttttgtttgttttatagcttttcattatgtgattatgtatgatt---tatatgtttttatcatttattag-----------------------
| | |||||||||||||| ||||| ||||||||| |||||| ||| || |||||||| || || || || || ||  | |||| |||  |||| || |||||| |  |     ||| |   || |||||  | || ||| || |  ||   ||| | |  || | |   |  | |||||| || || || |                        
ATCCATGGTGCAACAAGCAATGCAGTATATTGATCAGACACTAGACATAGAAACTCGGATTGAGCTTATTAAGACTCTAAACAATGTAGCTGCTGGAAAGgtgcggat-tagagttggctattgttgttgttgttgtag-ttatatttgcttgaatcttgatcactccgtgcaagtttttttc-ttgatgaatatgtgtgtgtgagcatgtgtag

upper sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 3
AGCTATGGTGCAACAAGCTATGCAATATATTGATGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc-------tatgtttgaactttttgtttgttttatagcttttcattatgtgatta--tgtatgatttat-atgtttttatcatttattag
 || ||||| || ||||||||||| ||||||||  ||||||| ||||| ||| ||   || || ||||| |||||  | ||||||||||||||||| |||||   |           || |||| | ||| |  | ||||  | |   |||  || |||  | |  | | |  || || || | |  || |||   |||
TGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTGCAGGAAAGgtcaatacatatatctataagtttcagcttatattatgttggacaatgtttttttttgttttgagctttttagttaattatatctgcattattatgtag

upper sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 3
lower sequence: PP1S58_256V6.1 (Physcomitrella patens), 5'ss of exon 3
AGCTATGGTGCAACAAGCTATGCAATATATTGATGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgctatgtttgaactttt-tgtttgttttatagcttttcattatgtgat----tatgtatgatttatatgtt--tttatcatttattag--------
 || |||||||| ||||||||||| ||||||||||| || |||||  | |||||||| || ||  | ||  | ||  | |||| ||| ||||||||||||||     | |  ||| |||    |    |    || ||    |    ||  |   |    | || |   | |  || ||  || ||| ||  ||          
TGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTGCAGGGAAGgtactctttcgttgtctgattgctcacatactcttgatgatatcatgttgagcagtgtcttttgaacagtatccatattgattcatcgttggttttattggtag

upper sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 3
lower sequence: PP1S257_89V6.2 (Physcomitrella patens), 5'ss of exon 3
AGCTATGGTGCAACAAGCTATGCAATATATTGATGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgctatgtttgaactttttgtttgttttatagcttt-tcattatgtgattatgtatgatttatatgtttttatcatttattag---------------------
  | |||||||| ||||||||||| ||||| ||||| || |||||| | |||||||| || | ||| ||| | ||  | |||| |||||| || || |||||       |||| ||| |    ||| || |||| |||   |  |  ||||||   | || || |||    || | |  |     ||||                      
TTCAATGGTGCAGCAAGCTATGCAGTATATAGATGAAACTCCAGATGTTGAAACTCGTATTGCACTGATCGAGACTCTCAACACTGTGTCCGCTGGAAAGgtt------ctatttttta----ttttttagtttcataatctcgttgttatgttcctgtg-ataattccagtggtatcgttggaaattaaaattttctctcgctctcgctc

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|27426310|gb|CA937830.1|CA937830
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|37996134|gb|CF807723.1|CF807723
EST:     AAACTCGCATAGAACTCATCANAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|5342415|gb|AI794699.1|AI794699
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|120496298|gb|EH224465.1|EH224465
EST:     CAGTGTGTCGGCAGGGAAG                         ATATCCAAGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: CAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|19271260|gb|BM887516.1|BM887516
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|18039945|gb|BM308239.1|BM308239
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|24206051|gb|BU965304.1|BU965304
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|26047818|gb|CA784480.1|CA784480
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|37997022|gb|CF808611.1|CF808611
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|17519815|gb|BM188857.1|BM188857
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|7925406|gb|AW831371.1|AW831371
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|308098502|gb|HO760243.1|HO760243
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|151401327|gb|EV271141.1|EV271141
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|23731285|gb|BU763760.1|BU763760
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|7795120|gb|AW780517.1|AW780517
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|192295223|gb|FG986942.1|FG986942
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|192309222|gb|FG999449.1|FG999449
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
EST: gi|192299616|gb|FG989998.1|FG989998
EST:     AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAG                         ATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT
genomic: AAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgc ... catttattagATATACGTGGAAATTGAGAGAGCTAGATTGATCAAGAAACTTGCAAAGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTATGGTGCAACAAGCTATGCAATATATTGATGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTGCAGGGAAGgtgggtgtgctatgtttgaactttttgtttgttttatagcttttcattatgtgattatgtatgatttatatgtttttatcatttattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG