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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatttcatttccttttcaaagtttgatatgagatacaaataattatgttttgggagtactaatcaataataaaattccttgtttttagAGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTTGCAGCTCGTATTCAGAAGCAGTTATTGCCATCCGACATTTGCCAGGACA

Basic information

species Glycine max
transcript GLYMA08G45960.1
intron # 6
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|120531567|gb|EH259700.1|EH259700
EST:     ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAG                         AGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
genomic: ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAGgtaatatttc ... ttgtttttagAGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
EST: gi|51341167|gb|CO982484.1|CO982484
EST:     ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAG                         AGTTTGNNAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
genomic: ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAGgtaatatttc ... ttgtttttagAGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
EST: gi|254331676|gb|GR846093.1|GR846093
EST:     ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAG                         AGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
genomic: ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAGgtaatatttc ... ttgtttttagAGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
EST: gi|120530846|gb|EH258979.1|EH258979
EST:     ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAG                         AGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
genomic: ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAGgtaatatttc ... ttgtttttagAGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
EST: gi|254331675|gb|GR846092.1|GR846092
EST:     ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAG                         AGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
genomic: ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAGgtaatatttc ... ttgtttttagAGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
EST: gi|26047413|gb|CA784215.1|CA784215
EST:     ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAG                         AGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT
genomic: ATATGCACATAATTCCTCGTAAAGCATATGATTGCTTATGGGCTTCTGAGgtaatatttc ... ttgtttttagAGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaaataattatgttttgggagtactaatcaataataaaattccttgtttttagAGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTTGCAGCTCGTATTCAGAAGCAGTTATTGCCATCCGACATTTGCCAGGACA
                       tactaat  putative branch site (score: 1)
                                         ttccttgttttt  putative PPT
                          taatcaataataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatttcatttccttttcaaagtttgatatgagatacaaataattatgttttgggagtactaatcaataataaaattccttgtttttagAGTTTGCTAAGGCGACGCCTTAATTTAGAGGATGAGAAAGTTTCTCAGCTTGCAGCTCGTATTCAGAAGCAGTTATTGCCATCCGACATTTGCCAGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC