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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcgcatccgtttattttctcttcgtcgtgtttaatgctgcgctctgcgtactctgtttataacggcgatatttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC

Basic information

species Glycine max
transcript GLYMA16G03170.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 3'ss of exon 3
-----gtattcgcatccgtttattttctcttcgtcgtgtttaatgctgcgctctgcgtactctgtttataacg-gcgatatttgttatc--tgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC
     |||||| |    |    ||      | || ||         |  | |  |    |||| |||  |  | | | ||||||  |    || || ||| || || || || ||||||||||||||  |||| ||||| |||||||| || || ||||| || |||||||| ||||| || || || 
gtatagtattc-ctcttgccccttcaaatattgtggtagcctccttttggtttggttagctctattttgatggtgtgctatttgcaaatcgtgtagCGGGCAAGACAGACTATCGTGCCAGGATTCGCCTGATCAATCAAGACAAGAATAAGTACAACACTCCAAAATATCGATTTGTCGTGCGATTT

upper sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 3'ss of exon 2
gtattcgcatccgttt---attttc-tcttcgtcgtgtttaatgctgcgctctgcgtactctgtttataacggcgatatttg---ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC
|||||    | | |||   || ||| |  |  | || |||     | || |    || | || |||||       || | |    || ||| |||||||||| || || ||| | || ||||||||  |||||||||| ||||||||||| |||||||| |||||||||||||||||||| || || 
gtattgtactacatttccaatgttcattcttatagtttttgggttttcgtt---tgttcgctttttatggatttaatttctaaaattgtctacagAGGGAAAGACTGACTACAGGGCTAGGATTCGCCTGATTAATCAAGACAAGAACAAGTATAACACTCCGAAATATCGCTTTGTTGTGCGATTT

upper sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S38_329V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------gtattcgcatccgtt-tattttctcttcgtcgtgtttaatgctgcgct-ctgcgtactctgttta---taacggcgatat--ttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC
                                                                                     |  | | |   ||  | | ||    |    || | |    ||| | |  |||||  |  |       | | || ||| |  |||||   |||||  || ||||||||||||||||| |||||||| |||| ||  ||||| |||||||| || ||||||||||| || || | ||| || || || 
gtgagtgggtttggtttgtgtttgggcatggattgttttgagtgacttgtttgtttttatctttagagtgtttggaattcaattttggttggaatggtggtgtgtttagattagggtttctggctctgggttgttgcgtttttcggaggagctgagggtgatgtggttgttga-tgcagCCGGTAAAACCGATTACCGTGCGAGGATTCGTTTGACTACCCAGGATAAGAACAAGTACAACACCCCGAAGTACCGTTATGTCGTGCGATTT

upper sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S364_3V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------gtattcgcatccgtttattttctcttcgtcgtgtttaatgctgcgctctgcgtactctgtttataacggcg-atatttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC
                                                                                      | | |||  |    |||||| |  |   ||||  ||||| |   | | |  |  |  | | |    |  |   ||   | |||||  || |||||||||||||| || ||||| || ||||  | ||||||||||||||| || ||||||||||| || || || || |||||||||
gtgcggatttttttgtggcatttgtcaccctcactgtcgaagatccttgatcttgaatcttttctgtgtgtcgttggtacagagggttgtatcgctggggtttctcgtt-ttaggttttctgctg-gtatttcttgttgcggatctgagattgtgtgcatggattatgcagCTGGTAAAACCGATTACCGGGCGAGGATCCGTTTGACCACTCAGGACAAGAACAAGTACAACACCCCGAAGTACCGTTTCGTCGTTCGTTTC

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|7041875|gb|AW471769.1|AW471769
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|4436984|gb|AI522849.1|AI522849
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|192315894|gb|FK008595.1|FK008595
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|13252441|gb|BG363352.1|BG363352
EST:     ACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|298198310|gb|HO039849.1|HO039849
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATT
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATT
EST: gi|15336852|gb|BI497508.1|BI497508
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|4397465|gb|AI496462.1|AI496462
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|19268986|gb|BM885242.1|BM885242
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|192308475|gb|FK001377.1|FK001377
EST:     ATCAAAAGCCTACTTCAAGAGGTATCGAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|209701098|gb|BW664200.1|BW664200
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|192317627|gb|FK007581.1|FK007581
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|7233168|gb|AW568517.1|AW568517
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|151393465|gb|EV263340.1|EV263340
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|18040030|gb|BM308324.1|BM308324
EST:     AAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: AAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|7284984|gb|AW597471.1|AW597471
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|15814259|gb|BI786534.1|BI786534
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|192315893|gb|FK008594.1|FK008594
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|151412354|gb|EV282166.1|EV282166
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|42722855|gb|CK768754.1|CK768754
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|192317628|gb|FK007582.1|FK007582
EST:     ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGGTATCAAGTCAAGTTCAAGAGAAGAAGAGgtattcgcat ... ttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatgctgcgctctgcgtactctgtttataacggcgatatttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC
                           ttataac  putative branch site (score: 2)
                                      atatttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcgcatccgtttattttctcttcgtcgtgtttaatgctgcgctctgcgtactctgtttataacggcgatatttgttatctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC