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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATACTGAAAGAGACGCAGCGGTGGTTGTAAGGCAGATGCTCAAGGTTGCAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcag

Basic information

species Glycine max
transcript GLYMA16G23870.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 5'ss of exon 3
TTATACTGAAAGAGACGCAGCGGTGGTTGTAAGGCAGATGCTCAAGGTTGCAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgc-tatacataatatattaatatttttacctattcttgcag
|||||  || | ||| || || || |||||  |||| |||||||||||||| |||||||| ||||| ||||||||||| || ||||||||||| || |||||||| || |  |    | ||   ||   |   || |   ||  |  ||  ||  |   | |||  |||  | |                              
TTATAGCGAGAAAGATGCTGCAGTAGTTGTGCGGCAAATGCTCAAGGTTGCTGCTGAGTGCCATTTGCATGGTTTGGTTCATCGGGACATGAAGCCTGAGgtatgctctaaaag---tacaagacta--agtcttcttataagagtaattgatcatttgatatgtgtatttacag-----------------------------

upper sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G365035_T01 (Zea mays), 5'ss of exon 4
TTATACTGAAAGAGACGCAGCGGTGGTTGTAAGGCAGATGCTCAAGGTTGCAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgagatcta-tactac-tagatgctatacataatatattaatatttttacctattcttgcag
||| |  || | ||| || || || |||||  | |||||||||||||||||||||||||| ||  | ||||||||||| || |||||||||||||| |||||||  ||    |   |   |||      ||   |||   ||||   |  |  || ||| |   |  || |   | ||   ||||| | |||    |   || ||
TTACAGCGAGAAAGATGCTGCAGTAGTTGTCCGACAGATGCTCAAGGTTGCAGCTGAGTGCCACCTGCATGGTTTGGTTCATCGGGACATGAAACCTGAGgtatactctgaaagtataagatag-----aatcctgtcataaatagtagttgctaatacctttttattaaaaggagta-gctaataatcttattggtg--tgtag

upper sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 6
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 5'ss of exon 4
TTATACTGAAAGAGACGCAGCGGTGGTTGTAAGGCAGATGCTCAAGGTTGCAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcag
||| || || | ||| |||||||| || || || || ||||| || ||||||||||| ||||||||||  ||| | || ||||| |||||||| ||||||||| |  | |     ||||  |   |||        ||  ||   | || |  |  |  |  | |   || | |   |    |||  |  | ||  ||  |||
TTACACCGAGAAAGATGCAGCGGTTGTGGTGAGACAAATGCTGAAAGTTGCAGCTGAATGTCATTTACGAGGTCTAGTTCACCGCGACATGAAGCCAGAGgtaggtacgattcagtttgattcaatgcttggaaattgcaaatccatatgtgaa--agcatcttcatcactttaagaagagttatgatcccttaccctctcag

upper sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 6
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 5'ss of exon 4
TTATACTGAAAGAGACGCAGCGGTGGTTGTAAGGCAGATGCTCAAGGTTGCAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaagcacatttgcat-atctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcag
|||||  || |||||||| || ||||| || || || ||||| || ||||| ||||||||||||||||  |||||||| ||||| || ||||||||||||||| | | ||  ||     ||| || |  |  | | ||||  | |  | | ||| |    |  |  | |   | |  || | || || | |   |         
TTATAGCGAGAGAGACGCGGCCGTGGTGGTGAGACAAATGCTGAAAGTTGCGGCTGAGTGTCATTTACGCGGTTTGGTTCACCGAGATATGAAACCAGAGgta-gcttaattactccatcatcatgtttctgaat-gtgtatagttggttttattca--caagtattgttttttac-taatcatcttctcaaacag--------

upper sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 5'ss of exon 4
TTATACTGAAAGAGACGCAGCGGTGGTTGTAAGGCAGATGCTCAAGGTTGCAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgag-atctatactactagatgctatacataatatattaatatttttacctattcttgcag
||||| ||| | ||| |||||    |||||||||||||||||||| ||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||| || |||     | ||| |  |   || ||||  |  |||  | | | ||  | |   ||| |        || |||    |||||| |   | | |   
TTATAGTGAGAAAGATGCAGCAAAAGTTGTAAGGCAGATGCTCAAAGTTGCAGCTGAGTGTCATTTACATGGTCTGGTACACCGTGACATGAAACCAGAGgtataatgaagtttgctggcacacatcaaaattttggctttaatttgtagccattatgcctaatggtgcttcccttacatt----tttttatcgcatgtag---

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|193524793|gb|FK482328.1|FK482328
EST:     CCGGGATATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193473081|gb|FK436670.1|FK436670
EST:     CAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193496517|gb|FK460703.1|FK460703
EST:     ATGGTTTGGTACACCGGGACATGAAACCAGAG                         AATTTTCTTTTTTAAATTCAACCAAAGAAGATTCACCTTTAAAGGCCACTG
genomic: ATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTC-TTTTTAAA-TCAACCAAAGAAGATTCACCTTTAAAGGCCACTG
EST: gi|193668943|gb|FK612271.1|FK612271
EST:     CCGGGACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|208080484|gb|GD878996.1|GD878996
EST:     CCGGGACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193451498|gb|FK417946.1|FK417946
EST:     ACATGAAACCAGAG                         AATTTTCTTTTTAAATTCAACCAAAGAAGATTCACCTTTAAAGGCCACTGA
genomic: ACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAA-TCAACCAAAGAAGATTCACCTTTAAAGGCCACTGA
EST: gi|193661924|gb|FK606938.1|FK606938
EST:     CCGGGACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193477388|gb|FK443525.1|FK443525
EST:     ACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: ACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193674208|gb|FK617300.1|FK617300
EST:     ACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: ACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATACTGAAAGAGACGCAGCGGTGGTTGTAAGGCAGATGCTCAAGGTTGCAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA