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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaatttttatgattgtgctcaatttgtggttcgaattatgagctttcgacactcacctcttccatttcacaaatttgaagtttccctcattctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTTTATCCTAACAATAAGGACAGTGTGGAGCTGATAAAATCACTCTTCCCCA

Basic information

species Glycine max
transcript GLYMA02G06380.1
intron # 5
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|193479031|gb|FK448044.1|FK448044
EST:     CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAG                         GCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
genomic: CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAGgtttgttctc ... attctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
EST: gi|17963160|gb|BM269912.1|BM269912
EST:     CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAG                         GCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
genomic: CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAGgtttgttctc ... attctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
EST: gi|11274284|gb|BF324652.1|BF324652
EST:     CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAG                         GCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
genomic: CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAGgtttgttctc ... attctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
EST: gi|208159060|gb|GD951785.1|GD951785
EST:     CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAG                         GCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
genomic: CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAGgtttgttctc ... attctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
EST: gi|192309386|gb|FK000594.1|FK000594
EST:     CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAG                         GCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
genomic: CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAGgtttgttctc ... attctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
EST: gi|58021399|gb|CX708140.1|CX708140
EST:     CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAG                         GCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
genomic: CTATTGCTTTTATGTACAATCCACCAAGAATATTCCAGGCTTTCTGGAAGgtttgttctc ... attctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
EST: gi|208143910|gb|GD943669.1|GD943669
EST:     CAAGAATATTCCTAGGCTTTTCTGGAAG                         GCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT
genomic: CAAGAATATTCC-AGGC-TTTCTGGAAGgtttgttctc ... attctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgacactcacctcttccatttcacaaatttgaagtttccctcattctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTTTATCCTAACAATAAGGACAGTGTGGAGCTGATAAAATCACTCTTCCCCA
      cactcac  putative branch site (score: 2)
 tttccctcattct  putative PPT
 aaatttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaatttttatgattgtgctcaatttgtggttcgaattatgagctttcgacactcacctcttccatttcacaaatttgaagtttccctcattctgatagGCCATCAGATTCTTCCTGGATCCCAAGACAGTCCAGAAGGTGAAGTTTGTTTATCCTAACAATAAGGACAGTGTGGAGCTGATAAAATCACTCTTCCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - gattgtg
- - - - - - - - - - - - - tgtggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccctc