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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatattgatcagagaaaatgagtctgaactatcttgcatatcaaaagagttagattagtatatgctctttcaaatgtaacacttataatttctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAAAGCATGTGAAATTTAGCAAACACATCAGTGCTGCTGCTGTTGCAACAAC

Basic information

species Glycine max
transcript GLYMA08G22740.1
intron # 1
splice site 3'
intron type U2

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|22540175|gb|BU090018.1|BU090018
EST:     TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTG                         TTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
genomic: TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTGgtcagtctct ... tctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
EST: gi|209725498|gb|BW677795.1|BW677795
EST:     TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTG                         TTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
genomic: TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTGgtcagtctct ... tctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
EST: gi|17519381|gb|BM188423.1|BM188423
EST:     TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTG                         TTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
genomic: TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTGgtcagtctct ... tctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
EST: gi|17400692|gb|BM177474.1|BM177474
EST:     TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTG                         TTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
genomic: TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTGgtcagtctct ... tctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
EST: gi|10232087|gb|BE800975.1|BE800975
EST:     TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTG                         TTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
genomic: TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTGgtcagtctct ... tctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
EST: gi|20448322|gb|BQ252446.1|BQ252446
EST:     TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTG                         TTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
genomic: TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTGgtcagtctct ... tctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
EST: gi|151400172|gb|EV269986.1|EV269986
EST:     TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTG                         TTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
genomic: TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTGgtcagtctct ... tctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
EST: gi|16105597|gb|BI893337.1|BI893337
EST:     TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTG                         TTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
genomic: TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTGgtcagtctct ... tctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
EST: gi|213608233|gb|DB970830.1|DB970830
EST:     TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTG                         TTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA
genomic: TTCCACGCAATCATGCTTGCCTGTGTCTCCTACCATTTCAAACACGCTTGgtcagtctct ... tctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttagattagtatatgctctttcaaatgtaacacttataatttctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAAAGCATGTGAAATTTAGCAAACACATCAGTGCTGCTGCTGTTGCAACAAC
                            atgtaac  putative branch site (score: 3)
                                           tttctcat  putative PPT
                               taacacttataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatattgatcagagaaaatgagtctgaactatcttgcatatcaaaagagttagattagtatatgctctttcaaatgtaacacttataatttctcatgcagTTAGTCCTTTTCTCAATGTTTCGTCACCAAGAAGTTACCTTGTGAAGAAAAAGCATGTGAAATTTAGCAAACACATCAGTGCTGCTGCTGTTGCAACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - agagaaaa
- - - - - - - - - -gagtctg
- - - - - - - - - - - - - - - - - tgcatat