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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGATACATATAAGAGTGATTTTGAGAATGAGAAGGCCTCTGGGAAATCTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataactgatgacattatatttcttctcaccccatcaattttgttggttgatattgtatgatatgctttatgctttatgttttatacttctttttgtgaacattaatatcgagcattttttcctacctttttcag

Basic information

species Glycine max
transcript GLYMA08G15340.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G15340.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 9
ATGGGATACATATAAGAGTGATTTTGAGAATGAGAAGGCC---TCTGGGAAATCTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataactgatgacattatatttcttctcaccccatcaattttgttggttgat---attgtatgatat-gctttatgctttatgttttatact-tctttttgtgaacattaatatcgagcattttttcctacctttttcag
| ||| | |||| ||| ||||| || |||||| | |||| || ||||| || ||||| |||||||||||||| || |||||||||||||||||| || || |||| | || | || |||||| ||| | | || | | ||| | | || ||| | | | ||| |||| || | |
---GAATATGTTTAAGGATGAATTTGAAAACGAGAAGAACATGCTTGGGGGCTCCTTGGGTGACAAAGCTGCAGAAGATCTAAGACAGAGAATAATTGAACATgtagtgtttctctg----tacatttagttccatacaat-aatttttttgatcatttgagttttgagttattgggtaattatttgtatgcaaaactgtcttcttttcag-----------------------------------
















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|27426694|gb|CA938214.1|CA938214
EST:     CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|209699016|gb|BW656131.1|BW656131
EST:     AAGGCAAAGAATAATTGAACAT                         AATATTC-TGTTNGTATCAAAATACTATGCAAGAATTACATTGAAGAGACT
genomic: AAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTT-GTATCAAAATACTATGCAAGAATTACATTGAAGAGACT
EST: gi|6724429|gb|AW308828.1|AW308828
EST:     AGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: AGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|9903102|gb|BE612070.1|BE612070
EST:     CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|23064146|gb|BU578919.1|BU578919
EST:     CAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|7640049|gb|AW734358.1|AW734358
EST:     CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|16347022|gb|BI972617.1|BI972617
EST:     AGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: AGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|151409280|gb|EV279088.1|EV279088
EST:     CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|15204177|gb|BI426945.1|BI426945
EST:     CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|21638863|gb|BM139909.1|BM139909
EST:     CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|209725253|gb|BW672728.1|BW672728
EST:     CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
EST: gi|17022111|gb|BM093145.1|BM093145
EST:     CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACAT                         AATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT
genomic: CTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataact ... cctttttcagAATATTCTTGTTGTATCAAAATACTATGCAAGAATTACATTGAAGAGACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGATACATATAAGAGTGATTTTGAGAATGAGAAGGCCTCTGGGAAATCTTTGGGAGAAAAAGCAGCAGAAGATCTAAGGCAAAGAATAATTGAACATgtaaataactgatgacattatatttcttctcaccccatcaattttgttggttgatattgtatgatatgctttatgctttatgttttatacttctttttgtgaacattaatatcgagcattttttcctacctttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA