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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttctgtataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactttggcag

Basic information

species Glycine max
transcript GLYMA11G12630.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12630.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G158887_T02 (Zea mays), 5'ss of exon 3
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttctgtataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactttggcag
 ||||| || || || ||||||||||| || || |||||||||||||| |||||||||||||||||||| ||||||||| | || || ||||| ||||| ||    | |      |   |   || ||   |||||     |||   | | |  | |||  ||     ||| || |    |  |                      
ATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCATTTGACAACCTGAATAACTGGCGAGAAGAGTTTCTAATTCAGgtgaaatatctccaatggtttattagttcagtctcacagcaatcctgtctttttatctaactt---tggatgtttccctctgcag---------------------

upper sequence: GLYMA11G12630.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G811797_T01 (Zea mays), 5'ss of exon 4
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttctgtataattttttctcagttttatctattatctca-agctatgttgtacagattttacaacttttaagatttgtgatcactttggcag
 ||||| || || || ||||||||||| || || |||||||||||||| |||||||| ||||| || ||| | |||||| | || || ||||| ||||| ||    |   |||     | || || |  ||      ||   |||   |  ||| | | ||  |||     |     |||| |  |  |||     ||||||| |||
ATTCTACCGGGGAGCAGATTGTTGTGTCCTAGTCTATGATGTTAATTCTATGAAATCGTTTGATAATCTTCACAACTGGCGTGAAGAGTTTCTAATTCAGgtgaaat---attttcaacggtttattagttcagtgattcagtctcacaattcataacaatcctgttttt-tcccctaactatggatgttt-----cactttg-cag

upper sequence: GLYMA11G12630.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G49300.1 (Arabidopsis thaliana), 5'ss of exon 4
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttctgtataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactttggcag
 || ||||||||||||||||| |||||||||||||||||||| || ||    |||||||| ||  | || || ||||||||||| || |||||||| || ||||   | |||     ||| ||   | | |||  |||       ||||     |   |  |||    ||  || |     ||  ||||||               
GTTTTATCGTGGTGCTGATTGCTGTGTTCTTGTATATGATGTCAACTCCGCAAAATCATTCGAGGATCTCAACAACTGGAGGGAAGAGTTTCTGATCCAGgtataaatatatatagatct-tactctctcttcctagtag-----attaaagagaaagaacttggcttgaaattgcggtaattgtgatttgcag------------

upper sequence: GLYMA11G12630.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G18820.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttctgtataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactttggcag
 || || |||||||||||||| |||||||||||||||||||| ||||| |||||||||||||| || || || ||||||||||| ||||||||||| || |||      ||||| |  |         ||||||||  | | |  |       |  | |   |   || | |  | ||    | ||   ||| ||  || | ||||
CTTTTACCGTGGTGCTGATTGCTGTGTTCTTGTATATGATGTCAATTCCATGAAATCATTTGAAAATCTGAACAACTGGAGGGAAGAATTTCTGATCCAGgta---acatattcatgcc---------ttttctcacctctgtagacagaagaattccacaataagca-actacataaacactgag---tgtaatatctcttgcag

upper sequence: GLYMA11G12630.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv03s0063g02420.t01 (Vitis vinifera), 5'ss of exon 5
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttat-tcctttctgtataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagat-ttgtgatcactttggcag
|||||| |||||||||||||| ||||||||||||||||||||||||  |||||| ||||||||||| || || || |||||||| |||||||| ||||| ||| | | |||| | ||||  ||||| |||  | |  |    |        ||    | |||     |   ||||  ||| |  | |      |||   |||      
TTTCTACCGTGGTGCTGATTGCTGTGTTCTTGTATATGATGTTAATGTGATGAAGTCATTTGACAATCTAAACAATTGGAGGGAAGAATTTCTCATTCAGgta-gttcttatgttcttttagtatattttacttttggccacagaagagggctactacgatgaaac-ctctttttggaacatgcatgtcaccatgagttctt------

upper sequence: GLYMA11G12630.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S61_279V6.1 (Physcomitrella patens), 5'ss of exon 3
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttc-tgtataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactttggcag
 || ||||||||||| ||||||||||||||||| || ||||| |||   ||||| || ||||| |||||| | ||||||||||| || ||||||||||| | | |  ||  ||  | || | || ||     | |  | |  ||| |   | | | |   |   ||   | ||| |    ||      | | |||  |  ||  |  
CTTTTATCGTGGTGCAGATTGTTGTGTTCTTGTCTACGATGTGAATGTTATGAAGTCTTTTGATAACCTTGACAACTGGAGGGACGAGTTTCTGATTCAGgcaagtattattttatatcatatacaaagagctttgtgatgaatcaagctttttatggagtac-gtctggctttcatgtattcc----tctttgaatatgttttc--

upper sequence: GLYMA11G12630.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S398_18V6.1 (Physcomitrella patens), 5'ss of exon 3
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttctg-----tataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactttggcag
 || || |||||||| ||||||||||| ||||| ||||| ||||||   ||||| |||||||| |||||| | |||||| |||| |||||| ||||||||||| | || ||   |    ||       |||  |||| ||  ||  | || || ||||  || |||  | ||| |||||    | || |||     | |            
CTTTTACCGTGGTGCAGATTGTTGTGTCCTTGTCTATGACGTTAATGTTATGAAGTCATTTGATAACCTTGAAAACTGGCGGGACGAATTTTTGATTCAAgtaagtttgtacctccaattggcaatcttaaaattttatctcttacacct-ttttctcttgccatgcaggacacattttctgtcattaaagcaacttaaat----------

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|254346570|gb|GR856292.1|GR856292
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192297090|gb|FG988186.1|FG988186
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192308782|gb|FG999793.1|FG999793
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTTTGATTCAA                         GCAAGTCCTTTTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|298169294|gb|HO020654.1|HO020654
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192322459|gb|FK014940.1|FK014940
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|58025186|gb|CX711927.1|CX711927
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|6726681|gb|AW311045.1|AW311045
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192308781|gb|FG999792.1|FG999792
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192294797|gb|FG987486.1|FG987486
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192319193|gb|FK006921.1|FK006921
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192299080|gb|FG992856.1|FG992856
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|151405344|gb|EV275158.1|EV275158
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192319192|gb|FK006920.1|FK006920
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|151410728|gb|EV280543.1|EV280543
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192315777|gb|FK008487.1|FK008487
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|31460535|gb|CD402503.1|CD402503
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACNAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|213605795|gb|DB968558.1|DB968558
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192299081|gb|FG992857.1|FG992857
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTTTGATTCAA                         GCAAGTCCTTTTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|151405872|gb|EV275687.1|EV275687
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|151395569|gb|EV265446.1|EV265446
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|254332273|gb|GR846318.1|GR846318
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|41146393|gb|CK606604.1|CK606604
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCCGATCCAGAGAATTTTCCTTTTGTTGCCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|7234184|gb|AW569523.1|AW569523
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|192315778|gb|FK008488.1|FK008488
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
EST: gi|254346571|gb|GR856293.1|GR856293
EST:     TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAA                         GCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA
genomic: TGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgctttt ... actttggcagGCAAGTCCTTCTGATCCAGAGAATTTTCCTTTTGTTGTCATAGGAAACAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTATCGTGGTGCTGATTGTTGTGTTCTTGTATATGATGTTAATTCGATGAAATCATTTGACAACCTTAATAACTGGAGGGAGGAATTTCTGATTCAAgtatgcttttattcctttctgtataattttttctcagttttatctattatctcaagctatgttgtacagattttacaacttttaagatttgtgatcactttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA