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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatttctgattgtttctttatggttttcatcatatttcataacttttgattttgttttattacctggaaattgatgatacccttgaaactggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGAAGAAGGGTCCTTCTCGGATAAGTGCCGTGACTGTTATATTTTACTTTTT

Basic information

species Glycine max
transcript GLYMA20G32530.4
intron # 1
splice site 3'
intron type U2

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|192325133|gb|FK017519.1|FK017519
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|192295767|gb|FG990847.1|FG990847
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|298189311|gb|HO037714.1|HO037714
EST:     GATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: GATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|192307320|gb|FK002384.1|FK002384
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|151402040|gb|EV271853.1|EV271853
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCCACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|208080337|gb|GD877141.1|GD877141
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGACCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|298192825|gb|HO033259.1|HO033259
EST:     CCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: CCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|10231625|gb|BE800513.1|BE800513
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|298167095|gb|HO010534.1|HO010534
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|151399368|gb|EV269239.1|EV269239
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|192313756|gb|FK007320.1|FK007320
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|17023121|gb|BM094155.1|BM094155
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|208174493|gb|GD971730.1|GD971730
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|192313755|gb|FK007319.1|FK007319
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|26058176|gb|CA801090.1|CA801090
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
EST: gi|192323408|gb|FK018999.1|FK018999
EST:     TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAG                         GTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA
genomic: TTCGATCCACTACGTGCCTGATCCTCTGCTTCAGGCACATACTCCCGCAGgttctacctc ... tggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgattttgttttattacctggaaattgatgatacccttgaaactggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGAAGAAGGGTCCTTCTCGGATAAGTGCCGTGACTGTTATATTTTACTTTTT
                        aattgat  putative branch site (score: 4)
     ttttgttttatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatttctgattgtttctttatggttttcatcatatttcataacttttgattttgttttattacctggaaattgatgatacccttgaaactggatattagGTTAAATGGCGAGGATCAAACCTCAGGCTCTGCTACAGCAAAGCAAAAGGAAGAAGGGTCCTTCTCGGATAAGTGCCGTGACTGTTATATTTTACTTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG