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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctaagcctttctctcagatttacgcttaacagagttacagtcactcagtaatctactccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCAGCCGAGTATGCTGGCGTCCAAGTTGATTTTGCCCCTAATTTTGAGATGG

Basic information

species Glycine max
transcript GLYMA17G00470.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00470.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------gtgagtctaagcctttctctcagatttac-gcttaacagagttacagtcactcagtaatct-actccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCAGCCGAGTATGCTGGCGTCCAAGTTGATTTTGCCCCTAATTTTGAGATGG
                           ||   |  | |  ||  |        ||| | ||| |    ||  | | |  || |  | | | |   |||  || || ||||||| |||||||| ||||||||| ||||||||||||||||||| || |||||    ||  || |||||||  | |  |  || ||||||||||
atttttgcaatttggggaagaaaagctgttgataaaggatttgattctgagcatactgattatctc--ttgaaataatacatttgtttgatttgctttgcagGTCTTGCATGCAGGGAAAACGAACAAAAATGCTTACAAGACACTCATTGCTGCGGAGTACAGCGGTATCAAAGTTGAACTGGTTCAGAACTTTGAGATGG
















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|254320830|gb|GR827279.1|GR827279
EST:     GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
genomic: GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
EST: gi|209713269|gb|BW684356.1|BW684356
EST:     GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
genomic: GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
EST: gi|213589446|gb|DB973182.1|DB973182
EST:     GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
genomic: GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
EST: gi|213599134|gb|DB962227.1|DB962227
EST:     GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
genomic: GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
EST: gi|192329687|gb|FK023275.1|FK023275
EST:     GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
genomic: GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
EST: gi|298185664|gb|HO030877.1|HO030877
EST:     GATCTTAATCAAGAGGAGTGAGTTTTGCTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
genomic: GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
EST: gi|5126554|gb|AI748290.1|AI748290
EST:     GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
genomic: GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
EST: gi|12773474|gb|BG238401.1|BG238401
EST:     TTAATCAAGAGGAGTGAGTGTTGTTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
genomic: TTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
EST: gi|192301560|gb|FG994772.1|FG994772
EST:     GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCGACAAAAATTCTTACAAGACACTCATTGCA
genomic: GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
EST: gi|9899280|gb|BE608248.1|BE608248
EST:     GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTG                         ATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA
genomic: GATCTTAATCAAGAGGAGTGAGTTTTGTTTTTCCAGCCATGACGCCGCTGgtgagtctaa ... ccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagatttacgcttaacagagttacagtcactcagtaatctactccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCAGCCGAGTATGCTGGCGTCCAAGTTGATTTTGCCCCTAATTTTGAGATGG
           gcttaac  putative branch site (score: 3)
                                       tctactccttttct  putative PPT
                                    taatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctaagcctttctctcagatttacgcttaacagagttacagtcactcagtaatctactccttttctagATCCTGCATGCTGGGAAAACCAACAAAAATTCTTACAAGACACTCATTGCAGCCGAGTATGCTGGCGTCCAAGTTGATTTTGCCCCTAATTTTGAGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG