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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaataggagcagtcaagtcattaagtatgcttgttgttttatatgatacctctctttcatgtttgggttacggcttttaactgaattttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA

Basic information

species Glycine max
transcript GLYMA18G47670.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 3
------------------aaataggagcagtcaagtcattaa----------gtatgcttgttgtttta-tatgatacctct-ctttcatgtttgggt-tacggctttt------aactg---aattttttttatgc-------tagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA
                  |  |||||| | |  |||     |          || | | || |||  || |    | |||   || | |  ||||| | |  |||| ||      | |||   |||||||||| |         |||||||| |||||||| || || || || || || ||||| ||||| ||||| ||||||||||| ||||||||||| ||   ||| ||   | | ||||||
gtactgattagtgatgtgagctaggaggatttgagtttcggaaatggcctctgtgtacctgctgtcctactgcattgccttggctgtgagatttggatgtgtggctgtttcttcgagctgttcaattttttttctttgctgatgtagATTGGAGATGAGACATTCATCATTGCTGCGCTGATGGCGATGCGGCACCCCAAGTCAATTGTGTTGTCTGGTGCACTATCTGCGCTTTATGTGATGACA

upper sequence: GLYMA18G47670.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G36290.1 (Arabidopsis thaliana), 3'ss of exon 4
aaataggagcagtcaagtcattaagtatgcttgttgttttatat-gatacctctctttcatgtttgggttacggcttttaactgaattttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA
            ||  ||   |   |||| ||   | ||    |  ||   |   |||  || || |         |||   |     | || |||| |||||||||||||| || ||||||||||| ||  | ||||||||||| || |||||  | | ||| || |||||||| |||   ||| || || | ||||| 
----------gttcgtgtgtgttgatatgattcaagcttagggtcaatttttagttttagtggttagagcttaatctttgttt---cgtattatatgttagATTGGGGATGAAACTTTTATAATAGCGGCATTGATGGCTATGCGACATCCTAAAGCTACTGTTTTATCTGGTGCACTCTCAGCTTTGTTTGTTATGACT

upper sequence: GLYMA18G47670.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 3
aaataggagcagtcaagtcattaagtatgcttgttgttttatatgat-acctctctt-tcatgtttgggtt--acggcttttaactgaattttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA
   |      |||  || |   || | |   ||| ||  | |||| | |||  | || | || ||||  |   | |  | ||   |  ||  |  |  |  |||||||| ||||| || ||||||||||||||||||||||| ||| | |||||||| |||||||| || |||||||| ||||||||| ||||| ||||||| 
---ttattatagt-gagcctcaaactgttactgtggtactgtatgtttaccagttttgttatatttgcatctgatgaatgttttattgataatggtgttattagATTGGAGATGAAACATTTATAATAGCAGCTCTTATGGCAATGAGACACCCTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG

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|192325593|gb|FK019449.1|FK019449
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagtttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
EST: gi|19935787|gb|BQ080586.1|BQ080586
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAG
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagtttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAG
EST: gi|19935946|gb|BQ080653.1|BQ080653
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagtttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCT
EST: gi|209709461|gb|BW668377.1|BW668377
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagtttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
EST: gi|19934369|gb|BQ079399.1|BQ079399
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagtttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
EST: gi|213605011|gb|DB956358.1|DB956358
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagtttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
EST: gi|193437896|gb|FK403567.1|FK403567
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagtttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT
EST: gi|254344439|gb|GR851136.1|GR851136
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCT-ATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagtttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacctctctttcatgtttgggttacggcttttaactgaattttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA
                             ttttaac  putative branch site (score: 2)
                                        ttttttttat  putative PPT
                             ttttaactgaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaataggagcagtcaagtcattaagtatgcttgttgttttatatgatacctctctttcatgtttgggttacggcttttaactgaattttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTTATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCTCTCAGTGCTCTGATTATAATGACA

- - - - gcagtca
- - - - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - -tgttgtt