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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgctcttatgtctcttttttttgttttttttgggaagcaggggggaggacgattcataattgaggtgggccttggggggaatcacgaggaggg...

Basic information

species Glycine max
transcript GLYMA17G17520.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g55490.1 (Oryza sativa), 5'ss of exon 4
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgctcttatgtctcttttttttgttttt--tttgggaagcaggg-gggaggacgattcataattgaggtgggccttggggggaatcacgaggaggg
| ||||||||||||||| | ||  ||||| | ||||| |||||||| || |||||||||||||||||   ||  |||||||||| | | || || |||||||   | | |  |    |     ||   |||||     |||   |||       || |    ||||       |     || |  | |        | |    
TCATGATTGATCATGAGAAACGCCAGCTTTGTCTTATTGATTGGGGTCTAGCAGAGTTCTATCATCCCAAGATGGAATATAATGCTAGAGTTGCTTCAAGgttagtctcccttgcattggaagttcaatgtttcagacttgttcagcttattaagaaggaacttcacttgcatgcctaaccctctgagatccttttatgt---

upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 4
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 5'ss of exon 4
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgta----catttgctcttatgtc--tcttttttttgttttttttgggaagcaggggggaggacgattcataattgaggtgggccttggggggaatcacgaggaggg
| ||||||||||| |||||||| || |||||  | || || |||||  | ||||| ||||||||||||||||||||||| ||||| ||||| || ||||||||    | ||||    | ||    ||| |  | ||     ||      |  |  |     |  |||  |  |    | | | || |    |||            
TCATGATTGATCACGAGCAGCGAAAACTTCGTTTAATTGACTGGGGTTTGGCAGAATTCTATCATCCTGGGAAAGAATACAATGTCCGTGTTGCTTCAAGgtagttccttttggctatctgctaatctctcctctgcaagattctatttgttgcagttgcta-aatttctgctcatagagagtctagataagaaatgttga-----

upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 4
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgctcttatgtctcttttt--tttgttttttttgggaagcaggggggaggacgattcataattgaggtgggccttggggggaatcacgaggaggg----
| ||||||||||||||||||||||| ||||| |||||||||||||| || |||||||||||||||||||| |||||||| |||||||| || || ||||||| | ||  | ||  | | |  |      ||  || |||||   || |         ||  ||  |  ||    | |   || ||  |||  || |          
TCATGATTGATCATGAGCAGCGTAAACTTCGTCTTATAGATTGGGGCCTGGCAGAGTTCTATCATCCTGGCAAAGAATACAATGTTCGGGTTGCTTCAAGgttctttccccctcttctttaatggaagcttaattattttgcatagtatattt----acatttttt--ttctccttgttttttggtagaactaccatttcctttct

upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 4
lower sequence: PP1S165_107V6.1 (Physcomitrella patens), 5'ss of exon 4
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgt--acat---ttgctctt--atgtctcttttttttgttttttttgggaagcaggggggaggacgattcataattgaggtgggccttggggggaatcacgaggaggg
| |||||||||||||| ||||| ||  |  |  | ||||||||||||||||| || ||||||||||| || ||||| ||||| || || || || || ||||   ||    |   || |  |||  || |        |||| |  | | ||              |  ||        |    ||||    |||||          
TGATGATTGATCATGAACAGCGAAAATTAAGATTAATAGATTGGGGGCTTGCTGAATTCTATCATCCCGGAAAAGAGTATAACGTGCGCGTTGCGTCTAGgtcagcacgcatcattcctgaatgcatcatcacaaaacttttctctgtacgctcttctagtttttttaaattcactttttaacacttgacttgaatcgtt-------

upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 4
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 5
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgctcttatgtctcttttttttgttttttttgggaagcaggggggagga--cgattcata-attgaggtgggccttggggggaatcacgaggaggg
|||||||||| || ||||| || |||||  | || || |||||||| || || ||||||||||| ||||| |||||||||||||| ||||| || || ||||| | ||         |||| |     ||| ||     || |         || |  ||  ||||| | ||  ||||    || ||   || |  |      
TAATGATTGACCACGAGCAACGAAAGCTGAGACTGATTGATTGGGGACTCGCTGAGTTCTATCACCCTGGCAAAGAATATAATGTGCGTGTTGCCTCCAGgta-agttctaaaggcttctcgtggcactgtcttaacgagggattcatttcaagaaatcgtatcatagaatgtagtggttactgtggattattattaattt--

upper sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 4
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 5
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgctcttatgtctcttttttttgttttttttgggaagcaggggggaggacgattcataattgaggtgggccttggggggaa---tca-cgaggaggg-
| |||||||| ||||||||||| |||||| | ||||| || ||||| ||||| || |||||||||||||| ||||| |||||||| ||||| || || ||||   |||   |  | |  ||||      |||  |  | || || |      |  | | ||        |   || | |  |    |    ||| |||| | |  
TGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACTGGGGACTTGCCGAATTCTATCATCCTGGCAAAGAGTATAATGTGCGTGTTGCCTCTAGgtgagttt---cagaggcttcttgaggcagttact--tagggaggactttatattatgtttggctgagaatccggacatcagaatcatgcttcatcgagtaagct

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|18734981|gb|BM528497.1|BM528497
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgc ... ttgcttgtagATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|9564123|gb|BE473632.1|BE473632
EST:     GCAGAGTTCTATCATCCTGNGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgc ... ttgcttgtagATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|21887281|gb|BQ740494.1|BQ740494
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgc ... ttgcttgtagATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|17963627|gb|BM270374.1|BM270374
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgc ... ttgcttgtagATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|13478623|gb|BG508028.1|BG508028
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAG                         ATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgc ... ttgcttgtagATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|18038926|gb|BM307220.1|BM307220
EST:     GCAGAGTTCTATCATCCTGNGAAAGAATATAATGTTCGTGTGGCATCAAG                         ATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgc ... ttgcttgtagATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|14260055|gb|BG882963.1|BG882963
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgc ... ttgcttgtagATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|9565463|gb|BE474972.1|BE474972
EST:     GCAGAGTTCTATCATCCTGNGAAAGAATATAATGTTCGCGTGGCATCAAG                         ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgc ... ttgcttgtagATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
EST: gi|254330876|gb|GR842141.1|GR842141
EST:     GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAG                         ATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC
genomic: GCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgc ... ttgcttgtagATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATGATTGATCATGAGCAGCGTAAGCTTCGCCTTATAGATTGGGGGCTTGCAGAGTTCTATCATCCTGGGAAAGAATATAATGTTCGTGTGGCATCAAGgtacatttgctcttatgtctcttttttttgttttttttgggaagcaggggggaggacgattcataattgaggtgggccttggggggaatcacgaggaggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA