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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCAAAACCAAATGTCATGCCATATGAAAAAGAGGAGCTGCTGAATGCTGCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAGggtaactatatttcattcaaaatcataaaatttgcttcaggctaatcagaaaaattcctgctgttctaccaagtctcaaattctaagaaaaaggtttatg...

Basic information

species Glycine max
transcript GLYMA17G37150.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G37150.1 (Glycine max), 5'ss of exon 12
lower sequence: AT1G75370.2 (Arabidopsis thaliana), 5'ss of exon 12
AGTCAAAACCAAATGTCATGCCATATGAAAAAGAGGAGCTGCTGAATGCTGCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAGggt---aactatatttc---attcaaaatcataaaatttgcttcaggctaatcagaaaaattcctgctgttctaccaagtctcaaattctaagaa-----aaaggtttatg
  || || |   |||  |||||   ||| ||||||||| |||| ||| | ||||||||||||||||||||| | |||||||| || ||||||||||| | |||   ||  | |  ||   |||| |  | | |  | ||   | |   ||||  |||||    |||   || |           ||  | || |      || | || |  
-CTCGAAGCGTCATGAGATGCCGCGTGAGAAAGAGGAGTTGCTTAATACAGCTGTTTATCGCGTGGATGCACTTGAAGCAGAGCTCATCGCTACAAAAAAGgtctaaaggaaacctctcaattccatgttaaatgacttttattaa-ttaatatgaaaagcaactgtctttgtgtgtgtatattaacgccaacactctccaatgattcag-

upper sequence: GLYMA17G37150.1 (Glycine max), 5'ss of exon 12
lower sequence: AT1G19650.2 (Arabidopsis thaliana), 5'ss of exon 11
AGTCAAAACCAAATGTCATGCCATATGAAAAAGAGGAGCTGCTGAATGCTGCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAGggtaactatatttcattcaaaatcataaaatttgcttcaggctaatcagaaaaattcctgctgttctaccaagtctcaaattctaagaaaaaggtttatg
  ||||    |   |  |||||  | || ||||||||| |||||||||||||||| ||||| ||||||||| | |||||||| || ||| | || |||| |||    | || |     |  ||  ||||   ||  | |   | ||   |  | |   |      ||   ||    | |||          | |   |  
-CTCAAGGAAATCCGAGATGCCTCACGAGAAAGAGGAGTTGCTGAATGCTGCTGTATATCGTGTGGATGCACTAGAAGCAGAGCTCATCACCACGAAGAAGgtttaaaaatctatgatatgattttaaaccctgaatgatattgat--aatgagtcattatgaaccttgtaataaccgaatatcggtgttgatgagcag-

upper sequence: GLYMA17G37150.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv18s0001g12950.t01 (Vitis vinifera), 5'ss of exon 12
AGTCAAAACCAAATGTCATGCCATATGAAAAAGAGGAGCTGCTGAATGCTGCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAGggtaactatatttcattcaaaatcataaaatttgcttcaggctaatcagaaaaattcctgctgttctac-caagtctcaaattctaagaaaaaggtttatg-
 | |||| |||      |||||  |||| ||||| ||| |||||||||||||||||| | | |||||||| || |||||||| || || |||||||||| |||||||  || | |    |  | ||  | |||||  |      ||    |||||   | |  | ||   |   | ||| |   | | ||||      ||| 
-GGCAAAGCCATTCAAGATGCCTCATGAGAAAGAAGAGTTGCTGAATGCTGCTGTTTGTAGGGTGGATGCCTTAGAAGCAGAGCTAATTGCTACAAAGAAGgtaacttcatctgaactgatttaattta-tttgcagcccatggatttacaaaatcaatacaatgcttttctgatttcacaaatttacaaaattagccatga

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|10231633|gb|BE800521.1|BE800521
EST:     CTGTTTATCGCGTGGATGCATTGGAAGCAGGACTGATCGCTACGAAGAAG                         GGCTT-ATATGAAGCTTTGATTATACAAGAAGAACTT
genomic: CTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGA-Gggtaactata ... tttctaaacaGGCTTTATATGAAGCTTTGATTAGACAAGAAGAACTT
EST: gi|58023387|gb|CX710128.1|CX710128
EST:     GCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAG                         GGCTTTATATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATCGA
genomic: GCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAGggtaactata ... tttctaaacaGGCTTTATATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATCGA
EST: gi|57575331|gb|CX548306.1|CX548306
EST:     GCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAG                         GGCTTTATATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATCGA
genomic: GCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAGggtaactata ... tttctaaacaGGCTTTATATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATCGA
EST: gi|19270862|gb|BM887118.1|BM887118
EST:     GCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAG                         GGCTTTATATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATCGA
genomic: GCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAGggtaactata ... tttctaaacaGGCTTTATATGAAGCTTTGATTAGACAAGAAGAACTTCTGGCATACATCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCAAAACCAAATGTCATGCCATATGAAAAAGAGGAGCTGCTGAATGCTGCTGTTTATCGCGTGGATGCATTGGAAGCAGAACTGATCGCTACAAAGAGggtaactatatttcattcaaaatcataaaatttgcttcaggctaatcagaaaaattcctgctgttctaccaagtctcaaattctaagaaaaaggtttatg

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaaa