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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG

Basic information

species Glycine max
transcript GLYMA01G36880.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactat---ttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
                     |  || || |||  | || || |  |  ||    ||||    || |  | ||| || |   ||     | |  | |||||||   | |   |   ||||||||||||| ||||||||||| || || || || |||||||||||||| |||||   ||  |||||||| || |||||||||||||| |
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccata-tatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG

upper sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------------------------------------------tattatttattatgaagtttggtt--aacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtat-ttgtatattta---aaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
                                                                                         |    || |    |    ||  |  | |  |  || |||| |  ||| ||||| |||||   | || ||  ||  | ||| || ||||| ||| |     ||||||||||||| ||||||||||| || || || ||||||||||||||||| |||||   || ||||||||| ||  | |||||||| || |
gtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagct-ttgtatctcattgaatcttgtaaattcatgtggaacagGATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAATGGAGCCACTGTGAATCTTGGGCTATGGGATACCGCAG

upper sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
lower sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
tattatttattatgaagtttggttaacgttttttgttttgtt-ttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
  |||| |   |   | | |  || | |||| ||||||  ||     ||  |  |  |   | | | |||  |   |||   |||||  ||    | ||||||||||||||| || ||||| || |||||||| || ||||| || || ||||| |||| ||||||||| || |||||||| ||||| |
-gttatgtcccaattattct--ttcatgtttcttgtttcattaccacaacaacaacatatctca-tgtttctt---gtttcttttgtggat----atacagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG

upper sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
---tattatttattatgaagtttgg----ttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
    |  || |   |  ||  ||      ||    |  ||  |||| || | | ||  |||   |  | | | ||| |||   ||| |||     |||   ||||||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||  || ||| || || || ||||||||||||||||
gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttattt--ttgaatt-----attgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG

upper sequence: GLYMA01G36880.4 (Glycine max), 3'ss of exon 1
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtat-atttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
                                  ||    ||| ||  ||  | ||   ||   | | | | |   |||   | | ||  || |  |||||||||| || || ||||||||||| || |||||||| |||||||||||| |||| | || ||| || || ||  | ||||| |||||||
----------------------------------gtgagatttcgttttgttctttccttt--ttctctaactctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG

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|37995833|gb|CF807422.1|CF807422
EST:     TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCANATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST: gi|17964056|gb|BM270797.1|BM270797
EST:     TGGGCAAAACCTGTTTGTTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST: gi|5175630|gb|AI759963.1|AI759963
EST:     TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST: gi|10843808|gb|BF067063.1|BF067063
EST:     TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCCCC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST: gi|7925509|gb|AW831535.1|AW831535
EST:     TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST: gi|5688224|gb|AI941239.1|AI941239
EST:     TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST: gi|21602816|gb|BQ613147.1|BQ613147
EST:     TGGGCAATACCTGAATGTTTATTTCCTACACCAGCAACACTTTTCCCACC                         GTATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAA
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagG-ATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAA
EST: gi|19452394|gb|BM953804.1|BM953804
EST:     TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST: gi|7684704|gb|AW755352.1|AW755352
EST:     TGGGCAAAACCTGGTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST: gi|17964054|gb|BM270795.1|BM270795
EST:     TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST: gi|298166464|gb|HO009903.1|HO009903
EST:     TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC                         GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG
                         attacgttgtatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA