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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatcgcgtttgattgcttgaacatgtttttatctttggtataattgttttcaccttttgatttcacactaatgaaatagttttttttttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTGAGCACAAGTATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCA

Basic information

species Glycine max
transcript GLYMA03G22220.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22220.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G09920.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------------------------------------------------ttgcatcgcgtttgatt------gcttgaacatgtttttatctttggtataattgttttcaccttttga----tttcacactaatgaaatagttttttttttttttcca---gAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTGAGCACAAGTATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCA
                                                                  | | || |   || |||      | || ||  ||   ||| || |     || |   || |   |||||    | |||    |||  |   ||||| || | |||  ||   |||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||| ||| |||||||| || |  || || ||||| ||||||||
gtacttctctattctcttcgccatatcccccgctgtgtacctcaaaattagggtttctttgcctcatcgaattgatcttaattcaatacgatttaat-tgagcttaactgtatcgaaaatcccttaattatttgagatttatcatcgaaattgatgggttttattctctttgacaaaagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTCTCTTTGATTCTTGAGCACAAGTTTGAACAGCTTCAGCAAATCTCAGAGGATCCTATGAATCA
















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|254340129|gb|GR858254.1|GR858254
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|6964421|gb|AW433114.1|AW433114
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|192308232|gb|FK001302.1|FK001302
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|192308233|gb|FK001303.1|FK001303
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|208159032|gb|GD951757.1|GD951757
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|298185814|gb|HO030975.1|HO030975
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGGACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|4289246|gb|AI441448.1|AI441448
EST:     GCCGCAGAGTTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: GCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|6964283|gb|AW432976.1|AW432976
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAAACG                         AGTTTTTGAAGGCGAAGTGCTTAATGAACTGGGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|193444022|gb|FK410272.1|FK410272
EST:     GAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTACTTAATGAA
genomic: GAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAA
EST: gi|208334499|gb|GE128762.1|GE128762
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|298168983|gb|HO020287.1|HO020287
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAGAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|208044561|gb|GD841041.1|GD841041
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|298164053|gb|HO013698.1|HO013698
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|151409001|gb|EV278809.1|EV278809
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|193386253|gb|FK350775.1|FK350775
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAACGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|208280986|gb|GE078874.1|GE078874
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|41145861|gb|CK606072.1|CK606072
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
EST: gi|208286434|gb|GE087822.1|GE087822
EST:     CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACG                         AGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG
genomic: CATGTCTGGGGAAGAGGAAGAAAACGCCGCAGAGCTCAAAATTGGAGACGgtaattaaac ... ttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttttcaccttttgatttcacactaatgaaatagttttttttttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTGAGCACAAGTATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCA
                       cactaat  putative branch site (score: 2)
                                  tagttttttttttttt  putative PPT
                 atttcacactaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatcgcgtttgattgcttgaacatgtttttatctttggtataattgttttcaccttttgatttcacactaatgaaatagttttttttttttttccagAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTTTCATTGATTCTTGAGCACAAGTATGAGCAGCTTCAACAGACATCCGATGATCCCATGAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
ttgcatc
- - - - - - tgattgc
- - - - - - - - - - - - catgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacacta