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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttacgaaatgttgttttctcatggaaatttactgtcatattgctttcatctttcaatttgttatctgggttgcaatcactgctaatttttattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGGATCATCACTGCATTCTGGGACATTCTAGCATTTGCATTACTCTGTGTTA

Basic information

species Glycine max
transcript GLYMA15G05370.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G05370.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g34360.1 (Oryza sativa), 3'ss of exon 3
----gttacgaaatgttgttttctcatggaaatttactgtcatattgctttcatctttcaatttgttatctgggttgcaatcactgctaatttttattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGGATCATCACTGCATTCTGGGACATTCTAGCATTTGCATTACTCTGTGTTA
     | |      | | |||| ||| || |||   ||||  ||| || ||     |   ||   | | |||   |||  |||    |   ||  ||||| ||||| || ||||| || |||||||| || | |||| | ||||| || || |||||||| ||||||||||||||| |||| |||||||  || ||   ||| |
ttcattcatctgcagattttttttca-gggaatcatctgttttatagcattatagctgtgataaataacctgctctgc--tcaacaatggcttc-attttgcagGTCTATTTCAAAGCGACAGATCCCTTTAGTGAGAGGTGGCAGAGCGCATGGATCATAACTGCATTCTGGGACGTTCTTGCATTTGTTTTGCTTCTTGTGA

upper sequence: GLYMA15G05370.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0034g01090.t01 (Vitis vinifera), 3'ss of exon 3
--gttacgaaatgttgttttctcatggaaatttactgtcatattgctttcatctttcaatttgttatc-tgggttgcaatcactgctaatttttattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGGATCATCACTGCATTCTGGGACATTCTAGCATTTGCATTACTCTGTGTTA
   | |  || ||||  | |   ||   ||   |   |  ||||  | |||  || |  ||    |   |   |||   |   |  |||  | | |  ||||||| ||||| ||||| || ||||| ||||||||||| ||||| |||||||||||||| ||||| || ||||||||||| || |||| ||| |||||||| |
tcttcattaactgttcatattatattataagacatgattttatt--tgtcactttactcttgaagactgttcattgttgttg-taataagctctttcctacagGTCTACTTTAAGGCAACGGATCCATTCAATGAGCGGTGGCAGAGTGCTTGGATCATTACTGCTTTTTGGGACATTCTTGCTTTTGGATTGCTCTGTGTCA
















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|58016452|gb|CX703194.1|CX703194
EST:     ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGG--ATGAG                         GTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
genomic: ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGGATATGAGgtaaggctta ... tattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
EST: gi|26269350|gb|CA820413.1|CA820413
EST:     ATGCATTAGCAGTAACGGTGATCTCCTCAGTTGCTTGGATAGGATATGAG                         GTATACTTCAAAGCTACAGATCCTTTCAATGAGCGCTGGCAGAGTGCTTGG
genomic: ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGGATATGAGgtaaggctta ... tattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
EST: gi|58018482|gb|CX705224.1|CX705224
EST:     ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTGGGATTGGATATGAG                         GTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
genomic: ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGGATATGAGgtaaggctta ... tattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
EST: gi|58019533|gb|CX706275.1|CX706275
EST:     ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGG--ATGAG                         GTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
genomic: ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGGATATGAGgtaaggctta ... tattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
EST: gi|51336251|gb|CO980117.1|CO980117
EST:     ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGGATATGAG                         GTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
genomic: ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGGATATGAGgtaaggctta ... tattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
EST: gi|9439998|gb|BE440509.1|BE440509
EST:     ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGGATATGAG                         GTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG
genomic: ATGCATTAGCAGTAACTGTGATCTCCTCAGTTGCTTGGATTGGATATGAGgtaaggctta ... tattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatctttcaatttgttatctgggttgcaatcactgctaatttttattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGGATCATCACTGCATTCTGGGACATTCTAGCATTTGCATTACTCTGTGTTA
                                   tgctaat  putative branch site (score: 2)
                                         tttttatttt  CT-rich tract
                                      taatttttattttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacgaaatgttgttttctcatggaaatttactgtcatattgctttcatctttcaatttgttatctgggttgcaatcactgctaatttttattttacagGTATACTTCAAGGCTACAGATCCTTTCAATGAGCGCTGGCAAAGTGCTTGGATCATCACTGCATTCTGGGACATTCTAGCATTTGCATTACTCTGTGTTA

- - - - -tgttgtt
- - - - - - - - - - catggaa
- - - - - - - - - - - - - - - tactgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgct