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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactgtgtctggctttttctagaacattctttccctttctcagcttatttagcttcaaatctgtttatttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATTGTGAGAATTAAACTTCTCCGAAATAAACCAGATCATGCACTTATTCAGA

Basic information

species Glycine max
transcript GLYMA20G30820.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30820.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g64770.5 (Oryza sativa), 3'ss of exon 11
gtaag----cactgtgtctggctttttctagaa-cattctttccctttctcagcttatttagcttcaaatctgtttatttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATTGTGAGAATTAAACTTCTCCGAAATAAACCAGATCATGCACTTATTCAGA
|||||    ||||   | |    | | | | |  || | |  |  | ||| || ||  |  | |   ||||  |  ||  |||| ||||||||||||||| || |||||||| ||||| || ||||||||||| ||| | || ||  | |||  |||||||||||||||||| || || ||||
gtaagatttcactagctataaactctcccaaattcactttaccaatatcttagttttatgggtt---aatccttccatg-cagAAAATTGATGAGGATAAGCTCTTCAACCTTTTCTCAATGTATGGGAATATCGTGCGTATCAAGATACTCAAAAATAAACCAGATCATGCCCTCATCCAGA

upper sequence: GLYMA20G30820.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------------------------------------gtaagcactgtgtctggcttttt---ctagaacattctttccctttctcagcttatttagcttcaaatctgttt-----atttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATTGTGAGAATTAAACTTCTCCGAAATAAACCAGATCATGCACTTATTCAGA
                                                      ||       | | |    ||||    || ||  |||| |    |  ||  |   ||  | ||   | || |||     |||||||||||| ||||| ||||| || |||||||||||||| || ||||| || ||||| |||||||| || ||||| ||||| ||||||||||||||  | || |
gtatgacttctctactcacccttcttcttcttcttcttcttcttcttctttatttatttttcctattttatcttttgtattaaaattttctgttggctcttctaccacttatgtttgggaactttttctgtcatttcagAGAATAGATGAAGATAAGCTTTTCAACCTGTTCTCCATCTATGGAAACATTGTCAGAATTAAGCTGCTCCGCAATAAGCCAGATCATGCACTAGTCCAAA
















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|17400944|gb|BM177726.1|BM177726
EST:     CTGGGACAAATGACAGGTGTACAGTTCTTGTATCAAATCTTAATCCTGAT                         AGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATT
genomic: CTGGGACAAATGACAGGTGTACAGTTCTTGTATCAAATCTTAATCCTGATgtaagcactg ... tttatttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATT
EST: gi|193584052|gb|FK540242.1|FK540242
EST:     CTGGGACAAATGACAGGTGTACAGTTCTTGTATCAAATCTTAATCCTGAT                         AGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATT
genomic: CTGGGACAAATGACAGGTGTACAGTTCTTGTATCAAATCTTAATCCTGATgtaagcactg ... tttatttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATT
EST: gi|9264616|gb|BE352763.1|BE352763
EST:     CTTGTATCAAATCTTAATCCTGAT                         AGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATT
genomic: CTTGTATCAAATCTTAATCCTGATgtaagcactg ... tttatttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATT
EST: gi|193653705|gb|FK595587.1|FK595587
EST:     CTGGGACAAATGACAGGTGTACAGTTCTTGTATCAAATCTTAATCCTGAT                         AGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATT
genomic: CTGGGACAAATGACAGGTGTACAGTTCTTGTATCAAATCTTAATCCTGATgtaagcactg ... tttatttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagaacattctttccctttctcagcttatttagcttcaaatctgtttatttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATTGTGAGAATTAAACTTCTCCGAAATAAACCAGATCATGCACTTATTCAGA
                                             tttatttc  CT-rich tract
                                      aaatctgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcactgtgtctggctttttctagaacattctttccctttctcagcttatttagcttcaaatctgtttatttcagAGAATTGATGAGGATAAACTATTCAACCTGTTCTCTATTTATGGGAATATTGTGAGAATTAAACTTCTCCGAAATAAACCAGATCATGCACTTATTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA