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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCAAATCCTTCTGTTGATGCCATCTTGCAAACAAAAGACTCGGTCCTTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcactctgtgaaatggccaaaacaaagagaagaaagaaagaatctgatatatgtttcagcattttccttttctgcgatctcaatatgatgtgctgatgttgtgatagtatatggtttgctatccactttatgattcatgcag

Basic information

species Glycine max
transcript GLYMA17G01300.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01300.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
TGCTGCAAATCCTTCTGTTGATGCCATCTTGCAAACAAAAGACTCGGTCCTTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcactctgtgaaatggccaaaacaaagagaagaaagaaagaatctgatatatgtttcagcattttccttttctgcgatctcaatatgatgtgctgatgttgtgatagtatatggtttgctatccactttatgattcatgcag
|||||| ||||| |||   ||  | ||||||   |  |||||  | || ||||||||||| ||||| || ||||||||| || |||||||||| ||| ||||||   |   |  | ||  |  |       |     |        | | |||| ||    ||   |||| |||   |  ||| | | |    | || | || || | |                                      
TGCTGCCAATCCATCTACAGACCCAATCTTGTCTAGCAAAGAAGCTGTTCTTGACAAGCTTTGGGAAATCAATGTCAAATCCTCTATACTTCTCCTGCAGgtaa---agcttccgtaagtgttagctttttgtttccatg------acccgatagat----caat-tttttcttagatttgatttgactcctctatgtttattttatcag-------------------------------------
















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|207787940|gb|GD762536.1|GD762536
EST:     CAAAGCCACTATACTTCTTCT-NAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: CAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|213610998|gb|DB970925.1|DB970925
EST:     TTGACAAGCTATGGGAGATAGATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|192297685|gb|FG989949.1|FG989949
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|192334495|gb|FK025588.1|FK025588
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|21889867|gb|BQ743080.1|BQ743080
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|6914599|gb|AW396129.1|AW396129
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|151412670|gb|EV282482.1|EV282482
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|27426906|gb|CA938426.1|CA938426
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|19348737|gb|BM893269.1|BM893269
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|298165658|gb|HO008629.1|HO008629
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|298171393|gb|HO016425.1|HO016425
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|209721713|gb|BW682554.1|BW682554
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|298172242|gb|HO021834.1|HO021834
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|298191832|gb|HO035914.1|HO035914
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGCTATCATT
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATT
EST: gi|298188159|gb|HO034852.1|HO034852
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|209708639|gb|BW678816.1|BW678816
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|151401904|gb|EV271717.1|EV271717
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|31470742|gb|CD412770.1|CD412770
EST:     TNGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|209725096|gb|BW663049.1|BW663049
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|10252762|gb|BE820528.1|BE820528
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|298171783|gb|HO021375.1|HO021375
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|308099226|gb|HO761404.1|HO761404
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|21285412|gb|BQ473283.1|BQ473283
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|298180281|gb|HO021892.1|HO021892
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|254327947|gb|GR834912.1|GR834912
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|13480380|gb|BG509723.1|BG509723
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|213592751|gb|DB955853.1|DB955853
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|298186690|gb|HO037323.1|HO037323
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|298178739|gb|HO024474.1|HO024474
EST:     TTGACAAGCTACGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|4306218|gb|AI443873.1|AI443873
EST:     TTGACAAGCTATGGGAGATAA-TGTCAAAGCCACTATACTTCTTCTGAAG                         GGAC-CAGTGCCTCACTTGC
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagG-ACGCAGTGCCTCACTTGC
EST: gi|192330812|gb|FK021599.1|FK021599
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|31310986|gb|CD396189.1|CD396189
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
EST: gi|254327948|gb|GR834913.1|GR834913
EST:     TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAG                         GACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA
genomic: TTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcact ... attcatgcagGACGCAGTGCCTCACTTGCAGAAGGGTTCTTCTGTTGTTATCATTTCCTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGCAAATCCTTCTGTTGATGCCATCTTGCAAACAAAAGACTCGGTCCTTGACAAGCTATGGGAGATAAATGTCAAAGCCACTATACTTCTTCTGAAGgtaattcactctgtgaaatggccaaaacaaagagaagaaagaaagaatctgatatatgtttcagcattttccttttctgcgatctcaatatgatgtgctgatgttgtgatagtatatggtttgctatccactttatgattcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG