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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAAGCCCTAGCAAAGGAACTAAGTGCTAAAGGGCAACTGCACAACATGCATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgttccccaatgctttgattcctgctctccatgtaagtttggaataaaaaaagtttatatggcatcatgatgttatcatattttgctggccccc...

Basic information

species Glycine max
transcript GLYMA06G06030.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G06030.2 (Glycine max), 5'ss of exon 5
lower sequence: AT2G26280.1 (Arabidopsis thaliana), 5'ss of exon 6
ATAAAGCCCTAGCAAAGGAACTAAGTGCTAAAGGGCAACTGCACAACATGCATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgttccccaatgctttgattcctgctctccatgtaagtttggaataaaaaaagtttat-atggcatcatgatgttatcatattttgctggccccc-------------------------------------------
|||| ||| |||| || || ||||||| ||| || ||  |||| || ||||| ||||||| ||||||||| |||||||||||| ||||||||| |||||||||||   |       |||  ||    || ||    |  | |  ||  |    ||| |     | ||  |  ||| |    |  | |     |  |  | |                                           
ATAAGGCCTTAGCCAAAGAGCTAAGTGTTAAGGGACAGTTGCATAATATGCAAATGAAGGCTGCTCATGGGAAAGCTCAAGAAGCCATTTACCGCCAGAGgtttgacttctttacctgcactg-catctccttgtaacatgatcttttatccgaaacacacactgatatctccataaatgaaaaacaaaactcctgttctcagtatctctgttctaacctgcctatgagtaaaaaatgaaacag

upper sequence: GLYMA06G06030.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv04s0008g02100.t01 (Vitis vinifera), 5'ss of exon 5
ATAAAGCCCTAGCAAAGGAACTAAGTGCTAAAGGGCAACTGCACAACATGCATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgttcccca-atgctttgattcctgctctccatgtaagtttgga--ataaaaaaagtttatatggcatcatgatgttatcat--attttgctggccccc
|||| || ||||| |||||||| ||   ||||||| | ||||||| ||| ||||||||||  ||||||||||||||||||||| | || || |  ||||||||||||    |  | |    ||| ||  |  |    |||  ||  |      || | ||  |||  || | ||  |  |   |  ||  || ||  |       
ATAAGGCACTAGCTAAGGAACTGAGCCTTAAAGGGAAGCTGCACAGCATTCATATGAAGGCAGCTCATGGAAAAGCTCAAGAAGCTATCTATCGTCAGAGgtttgttaactcttacagatcttgtttggttttagtgatgacagactaatttgtatataatatttggattggattttactaaaaatatccatctttttta-----
















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|66267155|gb|DR007282.1|DR007282
EST:     CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAG                         AAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
genomic: CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgtt ... attttttcagAAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
EST: gi|213602396|gb|DB981051.1|DB981051
EST:     CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAG                         AAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
genomic: CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgtt ... attttttcagAAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
EST: gi|23727551|gb|BU761810.1|BU761810
EST:     CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAG                         AAATCCAGTTGCTCCAGA
genomic: CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgtt ... attttttcagAAATCCAGTTGCTCCAGA
EST: gi|117557816|gb|EG702201.1|EG702201
EST:     CATATGAAGGTTGCTCATGGGAAAGCTCAAGAATCCATTTACCTCCAGAG                         AAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
genomic: CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgtt ... attttttcagAAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
EST: gi|214009325|gb|DB990615.1|DB990615
EST:     CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAG                         AAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
genomic: CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgtt ... attttttcagAAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
EST: gi|151409164|gb|EV278972.1|EV278972
EST:     CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAG                         AAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
genomic: CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgtt ... attttttcagAAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
EST: gi|6964547|gb|AW433240.1|AW433240
EST:     CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAG                         AAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT
genomic: CATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgtt ... attttttcagAAATCCAGTTGCTCCAGAGTTGCAGGGCGATGGAAGAGGAAATGAGAGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAAGCCCTAGCAAAGGAACTAAGTGCTAAAGGGCAACTGCACAACATGCATATGAAGGTTGCTCATGGAAAAGCTCAAGAATCCATTTACCTCCAGAGgtttgttgttccccaatgctttgattcctgctctccatgtaagtttggaataaaaaaagtttatatggcatcatgatgttatcatattttgctggccccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaaa