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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagatgcttcagtcttgtttccttctattagtaatagcaaatgtataagcttttggctacatgattggagtggagcaatcagctacggaaaccttcatgtccaattttctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGTTGAAGTAACAATTAGGAAAAAGGAGGCTATGCCTCAACCACCACCTCCT

Basic information

species Glycine max
transcript GLYMA09G38440.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38440.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g00760.t01 (Vitis vinifera), 3'ss of exon 3
gtaagcagatgcttcagtcttgtttccttctattagtaatagcaaatgtataagctttt--ggctacatgattggagtggagcaatcagctacggaaaccttcatgtccaattttctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGTTGAAGTAACAATTAGGAAAAAGGAGGCTATGCCTCAACCACCACCTCCT
                                | || ||   ||| |   ||  | ||   | |||  |||  |   |    ||| ||    | ||     || |||    || | |  ||||||||||||||||||||||| |||||||||||| || |||| |||| |||   |||| ||| |||| | |||||||||||  |||| ||||||||| |  ||
-------------------------------gtaagcaagctcaatttgttactccttgtagcctatttgacagttattcc-caaacatggtcagagcaaatcgtgttt--ttctgttttgcagGCTTGTTGATTCGAGAGATATTGTGGAGTTGCAGATGAAACAGCTTGACTGTGAACTAATAATTCGTAAAAAGGAGGCCTTGCCCCAACCACCATCAGCT
















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|16348210|gb|BI973805.1|BI973805
EST:     ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAA                         GCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
genomic: ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAAgtaagcagat ... tctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
EST: gi|213605948|gb|DB956648.1|DB956648
EST:     ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAA                         GCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
genomic: ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAAgtaagcagat ... tctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
EST: gi|8670260|gb|BE191367.1|BE191367
EST:     ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAA                         GCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
genomic: ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAAgtaagcagat ... tctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
EST: gi|213604876|gb|DB956161.1|DB956161
EST:     ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAA                         GCTTGTTGATTCGAGAGACATTGTGGAGTCGAAGCTGAAGCAGCATGATGT
genomic: ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAAgtaagcagat ... tctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
EST: gi|209714756|gb|BW654106.1|BW654106
EST:     ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAA                         GCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
genomic: ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAAgtaagcagat ... tctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
EST: gi|6134057|gb|AW132386.1|AW132386
EST:     ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAA                         GCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
genomic: ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAAgtaagcagat ... tctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
EST: gi|120529588|gb|EH257722.1|EH257722
EST:     ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAA                         GCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT
genomic: ACTCAAGAATCGGTCTCTCAGTTTATTACTCAAGTTGCAAGTCTTGTCAAgtaagcagat ... tctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattggagtggagcaatcagctacggaaaccttcatgtccaattttctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGTTGAAGTAACAATTAGGAAAAAGGAGGCTATGCCTCAACCACCACCTCCT
                                     tccaattttctcct  CT-rich tract
                                        aattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcagatgcttcagtcttgtttccttctattagtaatagcaaatgtataagcttttggctacatgattggagtggagcaatcagctacggaaaccttcatgtccaattttctcctgcagGCTTGTTGATTCGAGAGACATTGTGGAGTTGAAGCTGAAGCAGCATGATGTTGAAGTAACAATTAGGAAAAAGGAGGCTATGCCTCAACCACCACCTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG