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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgttcatgctatatgcaaatttgagctttcatctttacattttaatgtactgtctgagatttacaagtttttgaaatttgtgctttttgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC

Basic information

species Glycine max
transcript GLYMA04G39920.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39920.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g60780.2 (Oryza sativa), 3'ss of exon 1
ttatgttcatgctatatgcaaatttgagctttcatctttacattttaatgtactgtctgagatttacaagtttttgaaatttgtg----ctttttgatat---gcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC
   | |   | | |||||   |      |   || ||    |   |||  |  |  || || | || ||   |   ||| |          |  | || |    ||||||| ||  |||| ||||||||||| || || || |||||||||||||||||||| ||  | ||||   | || ||| |||||  ||| || |  ||  |
---tatgagtacaatatgacgaacaatac---cacctgagaaaactaac-tgtttcctaagctatataaccatgcaaaaatcacagcactctcctaatttctttcagCTACTACGCTGACAAGCTGGCATCTCCTGGTGACATTTTGTTCCCTTCATGTGGCTCTTCAGATGAAGCTTTTCGAGAACAAAGATTTAGACCCCAAGAC

upper sequence: GLYMA04G39920.4 (Glycine max), 3'ss of exon 2
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
ttatgttcatg-ctatatgcaaatttgagctttcatctttacattttaatgtactgtctga-gatttacaagtttttgaaatttgtgctttttgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC
  || || ||| || | |    ||   |||||| || |   | | |  |  |    ||| |  |  ||   ||| || |   ||||  ||||  || | |||| || |||||||| || ||||||||  | ||||| ||||||||||||||||||||  |    ||||   | || || ||||| |||||||| |    |||
-cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttctt-actcttgttattttgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC

upper sequence: GLYMA04G39920.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
ttatgttcatgctatatgcaaatttgagctttcatctttacattttaatgtactgtctgagatttacaagtttttgaaatttgtgctttttga---tatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC
      | | ||  ||   ||     | || | ||  ||  ||  |    ||   | ||   | |||  ||      |  || ||   |  |    | | ||||||| || ||||| ||||||||||| || ||||| || ||||| ||||||||||| ||    |||| ||| ||||| |||||||| |||||    |||||
--gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgct-tctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC

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|6724676|gb|AW309009.1|AW309009
EST:     CATTGTGATTTGCAATAAGGCGCTGATGAGTTCACTGCATTTCATTTTCG                         CTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG
genomic: CATTGTGATTTGCAATAAGGCGCTGATGAGTTCACTGCATTTCATTTTCGgtaactcaac ... tgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG
EST: gi|8282895|gb|BE020456.1|BE020456
EST:     CATTGTGATTTGCAATAAGGCGCTGATGAGTTCACTGCATTTCATTTTCG                         CTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG
genomic: CATTGTGATTTGCAATAAGGCGCTGATGAGTTCACTGCATTTCATTTTCGgtaactcaac ... tgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG
EST: gi|208330355|gb|GE132244.1|GE132244
EST:     AGTTCACTGCATTTCATTTTCG                         CTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG
genomic: AGTTCACTGCATTTCATTTTCGgtaactcaac ... tgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG
EST: gi|213597097|gb|DB968178.1|DB968178
EST:     CATTGTGATTTGCAATAAGGCGCTGATGAGTTCACTGCATTTCATTTTCG                         CTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG
genomic: CATTGTGATTTGCAATAAGGCGCTGATGAGTTCACTGCATTTCATTTTCGgtaactcaac ... tgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG
EST: gi|254319936|gb|GR829232.1|GR829232
EST:     GTTCACTGCATTTCATTTTCG                         CTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG
genomic: GTTCACTGCATTTCATTTTCGgtaactcaac ... tgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgtactgtctgagatttacaagtttttgaaatttgtgctttttgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC
                                      tgcttttt  CT-rich tract
                atttacaagtttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgttcatgctatatgcaaatttgagctttcatctttacattttaatgtactgtctgagatttacaagtttttgaaatttgtgctttttgatatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG