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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggcctacttttcagttccataactttcatttatttatgttgtgagtccttgttcatctgagttttgagcatttaaaaattgtgccgtgcag

Basic information

species Glycine max
transcript GLYMA08G46570.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46570.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G25040.1 (Arabidopsis thaliana), 5'ss of exon 5
CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaat--ttggcctacttttcagttccataactttcatttatttatgttgtgagtccttgttcat-ctgagttttgagcatttaaaaattgtgccgtgcag
|||||||  | ||  ||||||||||||| |||||||| || ||||||||||| ||||||| |||||||   ||  |  || ||||          ||||  ||   | | | | ||| | |||  ||   |||   ||   |  ||      || ||   |||||
CATGGATCGCCGGGTTTGTTCAAACACTGCTCTATGCCGACTTCTTCTATTATTATTTCCTAAGgtaacaattccctcacctttc----------cttttgttc-ctaacgctatgaattcttcctcggactgtaatt---gttttcccccgttatgat-tgcag

upper sequence: GLYMA08G46570.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv05s0029g00180.t01 (Vitis vinifera), 5'ss of exon 6
CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggcctacttttcagttccataactttcatttatttatgttgtgagtccttgttcatctgagttttgagcatttaaaaattgtgccgtgcag
| ||||| || || |||||||||||| | || |||||||||||||||||||| |||||||| ||||||        |||||||| |    |    |  || |   | | |  ||  |  || |     ||   |     ||||| ||   | | | |     
CTTGGATATCAGGGCTTGTTCAAACATTGCTTTATGCTGATTTCTTCTATTATTATTTCCATAGgtaacca---taacttttcaatctttttcaatcaatctcaatgtatgctggctgattttgttattggtctcactccattttaatggtttccag-----
















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|209715073|gb|BW677116.1|BW677116
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
EST: gi|193314107|gb|FK281742.1|FK281742
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAAAA-GCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
EST: gi|9564202|gb|BE473711.1|BE473711
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAG
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAG
EST: gi|31305448|gb|CD390651.1|CD390651
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
EST: gi|10252890|gb|BE820656.1|BE820656
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
EST: gi|21601718|gb|BQ612049.1|BQ612049
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGATTTTATTCTTCTGT
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
EST: gi|192306207|gb|FG996835.1|FG996835
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
EST: gi|27424798|gb|CA936318.1|CA936318
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAACAAGCTTCATTTGCCAGCA
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCA
EST: gi|208113393|gb|GD911578.1|GD911578
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CCGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
EST: gi|7147282|gb|AW509204.1|AW509204
EST:     CTTGGTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTGCAAAG                         CTGGAAGAACAACAAAAAGCTTCATTTGCCAGCA
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCA
EST: gi|8401987|gb|BE057621.1|BE057621
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
EST: gi|193612727|gb|FK560462.1|FK560462
EST:     CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG                         CTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT
genomic: CTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggc ... tgccgtgcagCTGGAAGAACAACAAAAAGCTTCATTTGCCAGCATGAGTTTATTCTTCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAGgtaatttggcctacttttcagttccataactttcatttatttatgttgtgagtccttgttcatctgagttttgagcatttaaaaattgtgccgtgcag

- - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - -  GCTGAT