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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttcaatcaatccctacactcactctcctttgcaattcccttcaattatgttgtttttgttgctccaaaatttgttgatcgattcaattatggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGAAAAGCGTATCAAGAGCTTGTGAAGGATATTACGCCGCCTAAGGATGTTC

Basic information

species Glycine max
transcript GLYMA20G31840.2
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|120530301|gb|EH258435.1|EH258435
EST:     TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAG                         AGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
genomic: TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAGgtctgttcaa ... tggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
EST: gi|298187634|gb|HO034783.1|HO034783
EST:     TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAG                         AGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
genomic: TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAGgtctgttcaa ... tggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
EST: gi|58016676|gb|CX703418.1|CX703418
EST:     AGCCCAGAGAGAAG                         AGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
genomic: AGCCCAGAGAGAAGgtctgttcaa ... tggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
EST: gi|58020292|gb|CX707034.1|CX707034
EST:     TAAGCCCAGAGAGAAG                         AGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
genomic: TAAGCCCAGAGAGAAGgtctgttcaa ... tggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
EST: gi|16996305|gb|BM085677.1|BM085677
EST:     TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAG                         AGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
genomic: TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAGgtctgttcaa ... tggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
EST: gi|13787967|gb|BG650559.1|BG650559
EST:     TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAG                         AGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
genomic: TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAGgtctgttcaa ... tggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
EST: gi|298193968|gb|HO040616.1|HO040616
EST:     TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAG                         AGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
genomic: TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAGgtctgttcaa ... tggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
EST: gi|192329380|gb|FK021834.1|FK021834
EST:     TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAG                         AGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA
genomic: TCTTTTCGGGCACCCGCTTCATCTTCTCCAGCCCTAAGCCCAGAGAGAAGgtctgttcaa ... tggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgttgtttttgttgctccaaaatttgttgatcgattcaattatggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGAAAAGCGTATCAAGAGCTTGTGAAGGATATTACGCCGCCTAAGGATGTTC
                           tgttgat  putative branch site (score: 4)
                     aaaatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttcaatcaatccctacactcactctcctttgcaattcccttcaattatgttgtttttgttgctccaaaatttgttgatcgattcaattatggtgtgaagAGTGAAGAATTGAAGGCGAGGCTGAAAAAGTTGGAAGACATAGCAGAGAGAAAAGCGTATCAAGAGCTTGTGAAGGATATTACGCCGCCTAAGGATGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG