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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttaatctttttgccttgtttaaaggttgcctctattgacaatttgacatggaatgcaatgcaataataattagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG

Basic information

species Glycine max
transcript GLYMA08G14780.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G14780.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G10070.1 (Arabidopsis thaliana), 3'ss of exon 6
atttaatctttttgccttgtttaaaggttgcctctattgacaatttgacatggaatgcaatgcaataataattagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
                    | | |  || |  ||  | ||   |  | ||| | | ||   |  ||  || | ||||  |  || |  | |  ||||||| |||||| | |||||||| |||||||||||||||||  | |||||| || |||| ||||| |||||||||||||| ||||| | | ||||
-------------------gtaagaacttacgact--taactgataaatatgta-tccagatctctaggaaat-gtttctaatttcttttatggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG

upper sequence: GLYMA08G14780.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g01200.t01 (Vitis vinifera), 3'ss of exon 6
-atttaatctttttgcct-tgtttaaaggttgcctctattgacaatttgacatggaatgcaatgcaata-ataattagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
    |||| |  |  ||| || |   ||  ||     |||| ||  ||    | |  |    |  |  |  |  | |   |  | | ||   |   |||||||| |||||||| || |||||||| ||||||||||||||||| |||||| |||| |||||||| || || |||||||| |||||    |||||
agagtaatgtgctcacctgtgatctcagaatgga---attgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG

upper sequence: GLYMA08G14780.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ23130 (Selaginella moellendorffii), 3'ss of exon 3
atttaatctttttgccttgtttaaaggttgcctctattgacaatttgacatggaatgcaatgcaataataattag-ttttcatattttccttttat-tgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
                                              |  |   | | |    |  |  |    || ||||  | |||| ||| ||  |||||||||||||||||| || || ||||||  ||||||||| ||||| ||  ||||||| || ||||| ||| |  | || ||  ||   || ||
----------------------------------------------gtaagttatttcctctctttgttctccagatttttttctttttcttgtacatgcagTGCCATGGCTTGTTGCTGCCAATCCAACAAATTATGGCCGGCCTTGCAAGCTATCGTGCGTAGAAGCTCTTACCGCGGCACTGGTTATTTG

upper sequence: GLYMA08G14780.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ20187 (Selaginella moellendorffii), 3'ss of exon 3
atttaatctttttgccttgtttaaaggttgcctctattgacaatttgacatggaatgcaatgcaataataattagttttcatattttccttttat-tgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
                                              |  |   | | |    |  |  |    || |||  | |||| ||| ||  |||||||||||||||||| || || ||||||  ||||||||| ||||| ||  ||||||| || ||||| ||| |  | || ||  ||   || ||
----------------------------------------------gtaagttatttcctctctttgttctccagattttttctttttcttgtacatgcagTGCCATGGCTTGTTGCTGCCAATCCAACAAATTATGGCCGGCCTTGCAAGCTATCGTGCGTAGAAGCTCTTACCGCGGCACTGGTTATTTG

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|192331293|gb|FK021004.1|FK021004
EST:     CTTAGATGACGTGTCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|192331294|gb|FK021005.1|FK021005
EST:     TAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: TAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|57574219|gb|CX547194.1|CX547194
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|298182193|gb|HO026368.1|HO026368
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|192320791|gb|FK013881.1|FK013881
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|298192264|gb|HO036346.1|HO036346
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|58022603|gb|CX709344.1|CX709344
EST:     TTTAGATGACGTGCCTTTCGTAGGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|192331184|gb|FK020951.1|FK020951
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|298191659|gb|HO039138.1|HO039138
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|192327943|gb|FK022474.1|FK022474
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTATTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|58018279|gb|CX705021.1|CX705021
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|298177830|gb|HO027383.1|HO027383
EST:     CTTAGATGACGTGC-TTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTCGTAGCAGCAAATCCAGTAAATTATGGTCGGCCGTGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|298178454|gb|HO024189.1|HO024189
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|208103050|gb|GD901488.1|GD901488
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|192331185|gb|FK020952.1|FK020952
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
EST: gi|298194036|gb|HO040684.1|HO040684
EST:     CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCT                         TGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC
genomic: CTTAGATGACGTGCCTTTCGTAAGGCTGCGCTGTACTGCTCCTCGCCTCTgtatgaactt ... tttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacatggaatgcaatgcaataataattagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
 atttgac  putative branch site (score: 4)
                              ttttcatattttcctt  putative PPT
                  aataataattagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttaatctttttgccttgtttaaaggttgcctctattgacaatttgacatggaatgcaatgcaataataattagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - -ttttgcc
- - - - - - - - - - - - - - tgcctct
- - - - - - - - - - - - - - - - - - - - - - -tgacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - atgcaat