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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttgcattttcgtttctgtatcttgttattatttaattgaatatttttttaggtattgtttttcttcttcttggatacttattaatatttagttgattggctcaagcttttatacataattttttgtttgtcactataaataattaaatatatggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGGAGAGCAAGATCATACAAAATAGCTAATGAGAACAACTAATACAAATCAA

Basic information

species Glycine max
transcript GLYMA16G29790.1
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|192320556|gb|FK011966.1|FK011966
EST:     ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGGCCCAAG                         GAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
genomic: ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAGgtcagttgca ... tggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
EST: gi|41146249|gb|CK606460.1|CK606460
EST:     ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG                         GAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
genomic: ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAGgtcagttgca ... tggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
EST: gi|58024886|gb|CX711627.1|CX711627
EST:     ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG                         GAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
genomic: ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAGgtcagttgca ... tggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
EST: gi|10256359|gb|BE824125.1|BE824125
EST:     ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG                         GAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
genomic: ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAGgtcagttgca ... tggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
EST: gi|31471135|gb|CD413163.1|CD413163
EST:     ATTCGGCCAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG                         GAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
genomic: ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAGgtcagttgca ... tggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
EST: gi|31475146|gb|CD417174.1|CD417174
EST:     ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG                         GAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
genomic: ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAGgtcagttgca ... tggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
EST: gi|9899031|gb|BE607999.1|BE607999
EST:     ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAG                         GAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG
genomic: ATTCGGAAAAATTCAATGGAGTGCCATATGGGCTGTTTTTGGGACCCAAGgtcagttgca ... tggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatacataattttttgtttgtcactataaataattaaatatatggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGGAGAGCAAGATCATACAAAATAGCTAATGAGAACAACTAATACAAATCAA
        ataattttttgtttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttgcattttcgtttctgtatcttgttattatttaattgaatatttttttaggtattgtttttcttcttcttggatacttattaatatttagttgattggctcaagcttttatacataattttttgtttgtcactataaataattaaatatatggcttgcagGAAATTGAAGAGGTGGGAGGGCTAGAAGAGCTGGAGAAAGAGATAAGTAGGAGAGCAAGATCATACAAAATAGCTAATGAGAACAACTAATACAAATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA