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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatttttctgttattttaaaagattaaaattctttacttgttactaggatttgcttgaatattctacacttaagttgatcaaactcttcgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCAATTAGAAGTTCTTTGCAGCATTTATGCTTTGTTTCTACTTCATAAGCAT

Basic information

species Glycine max
transcript GLYMA01G41600.1
intron # 12
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|6200959|gb|AW153059.1|AW153059
EST:     GATTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAA                         ATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
genomic: GATTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAAgtgagcttct ... cgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
EST: gi|213592086|gb|DB975236.1|DB975236
EST:     TTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGCGGTTTCCAA                         ATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
genomic: TTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAAgtgagcttct ... cgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
EST: gi|10255025|gb|BE822791.1|BE822791
EST:     GATTTAGTTGATGCNNNAGTTGCTCATTNNNAGTTAATCGTTGTTTCCAA                         ATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
genomic: GATTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAAgtgagcttct ... cgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
EST: gi|12773194|gb|BG238121.1|BG238121
EST:     GCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAA                         ATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
genomic: GCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAAgtgagcttct ... cgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
EST: gi|58017133|gb|CX703875.1|CX703875
EST:     GATTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAA                         ATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
genomic: GATTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAAgtgagcttct ... cgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
EST: gi|308222719|gb|HO760629.1|HO760629
EST:     GATTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAA                         ATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
genomic: GATTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAAgtgagcttct ... cgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
EST: gi|58018391|gb|CX705133.1|CX705133
EST:     GATTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAA                         ATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
genomic: GATTTAGTTGATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAAgtgagcttct ... cgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
EST: gi|19271160|gb|BM887416.1|BM887416
EST:     GATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAA                         ATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA
genomic: GATGCGGCAGTTGCTCATTGCCAGTTAATCGTTGTTTCCAAgtgagcttct ... cgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaggatttgcttgaatattctacacttaagttgatcaaactcttcgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCAATTAGAAGTTCTTTGCAGCATTTATGCTTTGTTTCTACTTCATAAGCAT
                             agttgat  putative branch site (score: 5)
 ctcttcgtttttt  putative PPT
 ttgaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaatttttctgttattttaaaagattaaaattctttacttgttactaggatttgcttgaatattctacacttaagttgatcaaactcttcgttttttagATTTATTGAGAAGTTGCAGCAAGATATCCCTGGAAAGGGAGTAAAAAAGCAATTAGAAGTTCTTTGCAGCATTTATGCTTTGTTTCTACTTCATAAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - -ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaact