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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataattgacttgtcttataccaaaaatttaggaatatcaatttcatttggaagaatttgcagaaaatggatacatcattgttgcttgctctaattgaactttcagtgacttgttttctaccccttttcagTGCTTCTTTCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTATTCATTCTTAATGCTGCTTATGATTCATGGCAG

Basic information

species Glycine max
transcript GLYMA03G38650.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38650.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G57590.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaataattgacttgtcttataccaaaaatttaggaatatcaatttcatttggaagaatttgcagaaaatggatacatcattgt-tgcttgctctaattgaactttcagtgacttgttttctaccccttttcagTGCTTCTTTCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTATTCATTCTTAATGCTGCTTATGATTCATGGCAG
                                            | ||| |     | ||  ||  ||||    |     | || ||||   |||  |   |  |  | |  | || |||| |     || ||||| || || || |||||| | ||   |   || |||||||| || || |||||||||||||| |||||||| ||||||
-------------------------------------------gtacatattcttaacttcacaccaaataagaaagatgtagtgtgctaaatctcctcataagtgtactc-catggtttcaata---ttgcagTGTTTTTTCCCACAAAACCTAATCAACCAAGTCAAGACTCCACTTTTTATTCTTAATGCTGCATATGATTCTTGGCAG
















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|208264654|gb|GE063974.1|GE063974
EST:     CACAGAAGAATCTGCCACAGATTTGTACTAATCACCTTGATCCCATCTCG                         TGCTTCTTCCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTATTACAT
genomic: CACAGAAGAATCTGCCACAGATTTGTACTAATCACCTTGATCCCATCTCGgtaataattg ... cccttttcagTGCTTCTTTCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTATT-CAT
EST: gi|192299205|gb|FG988663.1|FG988663
EST:     CACAGAAGAATCTGCCACAGATTTGTACTAATCACCTTGATCCCATCTCG                         TGCTTCTTTCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTATTCATT
genomic: CACAGAAGAATCTGCCACAGATTTGTACTAATCACCTTGATCCCATCTCGgtaataattg ... cccttttcagTGCTTCTTTCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTATTCATT
EST: gi|207780109|gb|GD753038.1|GD753038
EST:     CACAGAAGAATCTGCCACAGATTTGTACTAATCACCTTGATCCCATCTCG                         TGCTTCTTCCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTNTTCATT
genomic: CACAGAAGAATCTGCCACAGATTTGTACTAATCACCTTGATCCCATCTCGgtaataattg ... cccttttcagTGCTTCTTTCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTATTCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgttgcttgctctaattgaactttcagtgacttgttttctaccccttttcagTGCTTCTTTCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTATTCATTCTTAATGCTGCTTATGATTCATGGCAG
            ctctaat  putative branch site (score: 3)
                                 cttgttttctacccct  putative PPT
               taattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataattgacttgtcttataccaaaaatttaggaatatcaatttcatttggaagaatttgcagaaaatggatacatcattgttgcttgctctaattgaactttcagtgacttgttttctaccccttttcagTGCTTCTTTCCTCAAAACTTGATTGCCAGTGTTAAGACTCCGCTATTCATTCTTAATGCTGCTTATGATTCATGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT