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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccttctgtatttgtttatcttttacaatttatatgtatgaaggttttgaaagctttttgatactgatgggctttttgttcttggcaatgctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG

Basic information

species Glycine max
transcript GLYMA07G04040.1
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|192326234|gb|FK015826.1|FK015826
EST:     TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCTG
genomic: TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG
EST: gi|208308763|gb|GE104585.1|GE104585
EST:     TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCTG
genomic: TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG
EST: gi|192297449|gb|FG989513.1|FG989513
EST:     TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCTG
genomic: TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG
EST: gi|193553092|gb|FK507727.1|FK507727
EST:     TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCT
genomic: TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCT
EST: gi|298192744|gb|HO033178.1|HO033178
EST:     TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCTG
genomic: TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG
EST: gi|192333136|gb|FK026465.1|FK026465
EST:     TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCTG
genomic: TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG
EST: gi|298172302|gb|HO019342.1|HO019342
EST:     TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCTG
genomic: TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG
EST: gi|151405473|gb|EV275287.1|EV275287
EST:     TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCTG
genomic: TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG
EST: gi|18039623|gb|BM307917.1|BM307917
EST:     TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCTG
genomic: TAGGGATTTCAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG
EST: gi|120532679|gb|EH260812.1|EH260812
EST:     CAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTG                         ATGTTGAAGATTTTTACAACCAATGTGATCCTG
genomic: CAAGGGCCGAAGAGCTGGTCTCATCAAAGCCCTAACCACTGgtaaatcgtt ... gctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgaaagctttttgatactgatgggctttttgttcttggcaatgctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG
                 tactgat  putative branch site (score: 2)
          tttttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccttctgtatttgtttatcttttacaatttatatgtatgaaggttttgaaagctttttgatactgatgggctttttgttcttggcaatgctgttgcagATGTTGAAGATTTTTACAACCAATGTGATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
-gccttct
- - - - - - - - - - - - - - - - - -tgtatga
- - - - - - - - - - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatg