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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagtaacaatggagaatacatatgaaatgatgcttgataagctttgacattcttttctatttcgctaaatattgttattgttttctcttttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG

Basic information

species Glycine max
transcript GLYMA08G12970.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 15
aaagtaacaatggagaatacatatgaaatgatgc--ttgataagctt-tgacattcttttctatttcgctaaat--attgttattgttttctcttttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG
    |   | |     ||  || | ||| || |   || ||  | |  |||   | | |  | | ||  || |   |    ||   |    ||| ||| |  ||| |||||| | ||||||||  |||| |  ||  | |||||| | ||   ||| ||||||||||| |||||||| |||||||| |||||||||
----tgttagtcagccatctat-taaaaggaagaagttaatgtgttcctgaatgtgtgtaatttatcaatagagtaaccagtaaattcacttctgtttgctgcagCATGGGTCTTGACCTTTCAAAAGGTATCATTCGCAACAACCTTGAATATGGTGTCATTGAGCCAGCAATGAGTAAAGTAAAGATTATTCAG
















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|10844852|gb|BF071031.1|BF071031
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|58021211|gb|CX707953.1|CX707953
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|298168848|gb|HO009778.1|HO009778
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|193682839|gb|FK623867.1|FK623867
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|192311649|gb|FK004868.1|FK004868
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|298165014|gb|HO011063.1|HO011063
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|17021742|gb|BM092776.1|BM092776
EST:     ACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: ACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|10255075|gb|BE822841.1|BE822841
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|120495038|gb|EH223205.1|EH223205
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|192324297|gb|FK018273.1|FK018273
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|58022777|gb|CX709518.1|CX709518
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|58017859|gb|CX704601.1|CX704601
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|15200044|gb|BI424143.1|BI424143
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|51335203|gb|CO979069.1|CO979069
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|58019703|gb|CX706445.1|CX706445
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
EST: gi|151398434|gb|EV268305.1|EV268305
EST:     GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAG                         TATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG
genomic: GCCTACCACCATTCAGCACAAACTAAAGCCGATAAGAAACATTTATCAAGgtatttgctt ... ttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacattcttttctatttcgctaaatattgttattgttttctcttttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG
                  cgctaaa  putative branch site (score: 3)
                         tattgttattgttttc  CT-rich tract
                     taaatattgttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagtaacaatggagaatacatatgaaatgatgcttgataagctttgacattcttttctatttcgctaaatattgttattgttttctcttttttccccagTATGGGTTTGGACCTTTCTGAAGGGAAAATCAGAAACAACTTGGAGGCTGGAGTCATTGAGCCTGCAATGAGCAAAGTAAAAATTATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - -caatgga
- - - - - - - - - - - - - - tgatgct