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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacgcattcactcgctttctcggccaaaaattaaaaaaaaagagatgaattctgttttgtgctctctctgtttgattgtcctaaatcgaaacgcgcgtttcgttcttgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACGTGGCGAGGATCGAGCGGATCGAAGCCGACGCGCGCGGCTCCAACGTGAA

Basic information

species Glycine max
transcript GLYMA04G01140.1
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|298196200|gb|HO044591.1|HO044591
EST:     ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAG                         CTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
genomic: ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAGgtaaacgcat ... tgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
EST: gi|151404297|gb|EV274107.1|EV274107
EST:     ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAG                         CTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
genomic: ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAGgtaaacgcat ... tgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
EST: gi|4314010|gb|AI461129.1|AI461129
EST:     ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAG                         CTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
genomic: ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAGgtaaacgcat ... tgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
EST: gi|20811514|gb|BQ295992.1|BQ295992
EST:     GTCATACTCAGTCAAACACATAAGCAAAACCATTAGAG                         CTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
genomic: GTCATACTCAGTCAAACACATAAGCAAAACCATTAGAGgtaaacgcat ... tgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
EST: gi|298169727|gb|HO021087.1|HO021087
EST:     ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAG                         CTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
genomic: ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAGgtaaacgcat ... tgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
EST: gi|13562988|gb|BG551208.1|BG551208
EST:     ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAG                         CTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
genomic: ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAGgtaaacgcat ... tgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
EST: gi|13562907|gb|BG551127.1|BG551127
EST:     ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAG                         CTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
genomic: ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAGgtaaacgcat ... tgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
EST: gi|4297480|gb|AI442624.1|AI442624
EST:     ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAG                         CTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
genomic: ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAGgtaaacgcat ... tgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
EST: gi|298163162|gb|HO011895.1|HO011895
EST:     ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAG                         CTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG
genomic: ACGAACCCTAGAGTCATACTCAGTCAAACACATAAGCAAAACCATTAGAGgtaaacgcat ... tgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctctgtttgattgtcctaaatcgaaacgcgcgtttcgttcttgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACGTGGCGAGGATCGAGCGGATCGAAGCCGACGCGCGCGGCTCCAACGTGAA
                 tcctaaa  putative branch site (score: 2)
                                    tttcgttcttgtctct  putative PPT
         tttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacgcattcactcgctttctcggccaaaaattaaaaaaaaagagatgaattctgttttgtgctctctctgtttgattgtcctaaatcgaaacgcgcgtttcgttcttgtctctcagCTGGCGATTGCGTGCTCATGCGGCCCTCCGATCTGTCGAAACCGTCGTACGTGGCGAGGATCGAGCGGATCGAAGCCGACGCGCGCGGCTCCAACGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT