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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctctgaactgatataatagtattaagagattctttcagagctatttattgctatgttaagccatatttacttacatgcctgctgtggacactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA

Basic information

species Glycine max
transcript GLYMA02G08170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G08170.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g56210.1 (Oryza sativa), 3'ss of exon 3
-atctctgaac-tgatataatagtattaagagattctttcagagctatttattgc-tatgttaagccatatttacttacatgcctgctgtggacactggacagTGCTTGCTAGTGAAGGGATGGAAA---GGTTCAAGCTGGAGCTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA
 |||| | | | |  || |     |||     |||||||   |  |  | ||  | ||     | ||  | || | | ||    | ||       |||  ||||||||||| ||||||||||||||     |  | |||||||| || ||||||||||| | ||| ||||| |||||||||||| |||||||  ||||||||
gatctttaacccttgtagacctcaattcgcgcattctttttcactttgtcatcacatactcacaccccaagtttcattcactttttctcc---ttctgtgcagTGCTTGCTTGTGAAGGGATGGAAGTCTAGCGCCAGCTGGAGTTTTCCTCGTGGAAAGAGGAGTAAAGATGAAGAAGATCATACATGTGCTGTTAGAGAA

upper sequence: GLYMA02G08170.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G13570.1 (Arabidopsis thaliana), 3'ss of exon 3
atctctgaactgatataatagtattaagagattct-ttcagagctatttattgctatgttaagccatatttacttacatgcctgctgtggacactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA
               ||| |    |  | | |  | || ||   || |||||     |||||  | ||     ||   ||  |    | | || |   |||||| || | ||||||||||||||||| || ||||||||||| || || |||||||||||||| || |||||||| ||||| ||||||||  | || 
--------------gtaagaaccctgtggggtgatatttaggtttacttatta----gttaatgcttaccctttt---tgttt--cattgtcatttt-cagTGCCTGTTGGTGAAGGGATGGAAAGGATCGAGCTGGAGCTTTCCCCGCGGAAAAAAGAGCAAGGATGAAGAAGACCATGCTTGTGCCATACGTGAG

upper sequence: GLYMA02G08170.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g04310.t01 (Vitis vinifera), 3'ss of exon 3
----atctctgaactgatataatagtattaagagattctttcagagctatttattgctatgttaagccatatttacttacatgcctgctgtggacactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA
    ||  | ||  | || ||||||| | |||  | |  |||||  ||  || |    || ||  | || | |   ||  || | || | || | | |  ||||||||| ||||||||||||||||||||  |||||||||| || || ||||||||||||| |||||| |||||||| ||  | |||||||||||||||
acacataacagagtt-atctaatagtttgaagtaagtgattcagttctccttttaaaaatatt--gtcacact-gttttgatacttgttttgtataattaacagTGCTTACTAGTGAAGGGATGGAAAGGAACAAGCTGGAGTTTTCCCCGTGGAAAAAAGAACAAAGATGAAGAAGACCACACGTGTGCCATTAGAGAA

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|192322569|gb|FK014690.1|FK014690
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTCCAAGCTGGAGCTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... cactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
EST: gi|16106178|gb|BI893918.1|BI893918
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... cactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
EST: gi|151403573|gb|EV273383.1|EV273383
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... cactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
EST: gi|13789427|gb|BG652018.1|BG652018
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... cactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
EST: gi|193427446|gb|FK394858.1|FK394858
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTACAAGTTGGAGTTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... cactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
EST: gi|5509566|gb|AI856124.1|AI856124
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGACAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... cactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
EST: gi|151407825|gb|EV277640.1|EV277640
EST:     TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGG                         TGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA
genomic: TTCGAGTTCCTGTAACTGGGGCAATAATTCTTGATGAAACATATGAAAGGgtaagacaag ... cactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattgctatgttaagccatatttacttacatgcctgctgtggacactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA
                        tacttac  putative branch site (score: 1)
                   atatttacttacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctctgaactgatataatagtattaagagattctttcagagctatttattgctatgttaagccatatttacttacatgcctgctgtggacactggacagTGCTTGCTAGTGAAGGGATGGAAAGGTTCAAGCTGGAGCTTCCCTCGTGGAAAAAAGAGCAAAGACGAAGAAGATCATGCATGTGCCATTAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- ctctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - tgctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgtgg