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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAGGCAACATTCATCCCCAGGTTACAGATTCCCTTCTTCAAGAGCTTTTTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAGgtcagctttgtttatactttataatgaattaatgatatcttcaaagaaagaataaaatgatggagtgatatttgataatgtatgatagaattcatgattt...

Basic information

species Glycine max
transcript GLYMA17G05530.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05530.4 (Glycine max), 5'ss of exon 4
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 3
TGTAGGCAACATTCATCCCCAGGTTACAGATTCCCTTCTTCAAGAGCTTTTTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAGgtcagctttgtttatactttataatgaattaatgatatcttcaaagaaagaataa--aatgatggagtgatatttgataatgtatgatagaattc-atgattt
||| || || || || || |||||||||||  | |||||||||||| |||| || | | | ||  |||| ||||| |||||||| |||||||||||||||||||| |||  || | |    |   ||| | ||  | |      | ||  ||| |  | | |||   | ||| |  || ||  || |||| ||   ||| || 
TGTGGGTAATATCCACCCACAGGTTACAGAACCACTTCTTCAAGAGGTTTTCTCTAGTACTGGTCCCCTCGAAGGGTGCAAGCTCATTAGGAAAGAGAAGgtcagttttcattttgccgatttcagaaatcatctttttgatggataagcaatgaccagtcatgccat-atactatatgat-cataatagcatctgatggtt-
















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|193443462|gb|FK409208.1|FK409208
EST:     GGAAAGAGAAG                         TCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
genomic: GGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
EST: gi|193640436|gb|FK592779.1|FK592779
EST:     CCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAG                         TCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
genomic: CCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
EST: gi|207682231|gb|GD665302.1|GD665302
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
EST: gi|14126550|gb|BG790988.1|BG790988
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAG                         TCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
EST: gi|208308905|gb|GE101633.1|GE101633
EST:     CTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
genomic: CTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
EST: gi|7639266|gb|AW733592.1|AW733592
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAG                         TCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
EST: gi|193467443|gb|FK432556.1|FK432556
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
EST: gi|11274392|gb|BF324745.1|BF324745
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAG                         TCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGGTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTAGGCAACATTCATCCCCAGGTTACAGATTCCCTTCTTCAAGAGCTTTTTTCAACTGCAGGCGCCCTTGAAGGATGCAAGCTTATTAGGAAAGAGAAGgtcagctttgtttatactttataatgaattaatgatatcttcaaagaaagaataaaatgatggagtgatatttgataatgtatgatagaattcatgattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataaaa