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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttttttttaatctatttatttgtttatttttgggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAA

Basic information

species Glycine max
transcript GLYMA15G07570.2
intron # 3
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07570.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatccttttttttaatctatttatttgtttatttttg-ggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAA
||||||||||| | | |||  || |  |||| | |||  ||  |  | |||   ||  ||    |  |   |    | |||  |||||||| ||   |||||||| ||||||||||| || || || ||||| ||||||||||||||||| || ||||  || || || || ||||| ||||||||||| ||||| || ||
gtatcctttttctgattctggttttgagtttttgtttatggaattggtgtgtttgatgtttagcttatctactccttttgaacttccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA

upper sequence: GLYMA15G07570.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 8
gtatcctttttt---ttaatctatttatttgtttatttttgggtctatgagtgcaaga--gattgtattctttatccagctatga---ttttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAA
|||||||||| |   ||    |      ||  || | ||   | |||  ||||       |     ||||  | |  |||| | |   || |||||||||||  | ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||  |||| || ||||| ||||||||||| ||||| ||||| || ||
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA

upper sequence: GLYMA15G07570.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 6
gtatcctttttt---ttaatctatttatttgtttatttttgggtctatgagtgcaaga--gattgtattctttatccagctatga---ttttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAA
|||||||||| |   ||    |      ||  || | ||   | |||  ||||       |     ||||  | |  |||| | |   || | |||||||||  | ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||  |||| || ||||| ||||||||||| ||||| ||||| || ||
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcaatttttagctgtaaagcttattcttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA

upper sequence: GLYMA15G07570.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S268_9V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatccttttttttaat-ctatttatttgtttatttttgggtctatgagtgcaagagattgtattct-ttatccagctatgatt---ttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAA
    |        | || ||| | ||  ||  | ||   ||  | ||  | |      |   ||||| |||    |   || |    |||||||  ||   |||||||||||||||||||  || || || || ||||||||||||  |||||| |||||  ||||  | || |||||||| || || ||||| |||||||| ||
----ctgaacgaatgatgctaatgatcagtgaaattaaagggttgtgt-tactcattctgaaattctcttacagtgggctggtccaattccttagcgaggaacagCAGACATAGATCTTGGCACCATTACTGACCGCATGGCTGTTCGAAAGGCTGTACAGTGTGGACAGGTGGAAGATGCTATCGACAAAGTCAATGACTTGAA

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|193555708|gb|FK513255.1|FK513255
EST:     CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
genomic: CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
EST: gi|151408269|gb|EV278077.1|EV278077
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
EST: gi|298181140|gb|HO022579.1|HO022579
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
EST: gi|9819896|gb|BE555339.1|BE555339
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAAGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
EST: gi|193719536|gb|FK650872.1|FK650872
EST:     CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
genomic: CTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
EST: gi|15812571|gb|BI784846.1|BI784846
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
EST: gi|192297765|gb|FG989971.1|FG989971
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
EST: gi|207765821|gb|GD735462.1|GD735462
EST:     AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG
genomic: AGGCTATGTTGAAGCTGCTGAGAAATTCCGAATGGAGTCTGGAACTGAGCgtatcctttt ... tgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgcaagagattgtattctttatccagctatgattttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAA
 ttccttatt  putative branch site 
                                   ttttccttatt  putative PPT
           attgtattctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttttttttaatctatttatttgtttatttttgggtctatgagtgcaagagattgtattctttatccagctatgattttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG