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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagttatgtctagctactgctagtatcattggtcaataagttcatgtttatctgaccctgaaagactatctaatttataatgaaacaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG

Basic information

species Glycine max
transcript GLYMA15G04500.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 6
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
atagttatgtctagctactgctagtatcattggtcaataagttcatgtttatctgaccctgaaagactatctaatttataatgaaacaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG
             | |  ||  | |||   |      | |  |||  || || | | |     ||| |   || ||  | ||  || | |   | | |||||||| ||||| ||||||||||| ||||| |||||||| || || || ||||| || ||||||||
-------------gttcgtgtgaatatagatatattctcatatcaccttcatataatc-----agaatcgttagttactgatctaata-tgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG

upper sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 6
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
atagttatgtctagctactgctagtatcattggtcaataagttcatgtttatctgaccctgaaagactatctaatttataatgaaacaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG-----------------------------------
   ||| |||  | ||   | || |   |     ||| | | |      ||| |     |||   |  |||  || |    |  | |  |    |  ||||| ||||| |||||||||||||||||||| |||||| | || || ||||||||||| ||||||||                                   
---gtt-tgttaaact-tcgttaatcaaaactcgcaaaatgctagctgatatatttttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG

upper sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
atagttatgtctagctactgctagtatcattggtcaataagttcatgtttatctg---accctgaaagactatctaa-tttataatgaaacaattacttta-cagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG
    | | ||||||  | |  | || |     |||| |    |||| |  |  ||   |   |  |  | | ||| | ||| | |   |||  | |||||| ||||||||||| ||||| || ||||| |||||||| ||||| || || || || ||||| ||||||||
---ttgacgtctag--attttttgtgttcaatgtcagtgcagtcatttgaacttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG

upper sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
atagttatgtctagctactgct-agtatcattgg--tcaataagttcatgtttatctgaccctgaaagactatctaatttataatgaaacaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG
 ||  ||| | ||   |    | ||  |   | |  | || |  |   ||  | || |   | ||  |  | |  |||||    ||||||  | | ||| ||||| || ||||||||||||||||| || || ||||||||||| |||||||| ||||| || |||||
-tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtt-tgaaatttggtttgaaact-tcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG

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|213611728|gb|DB962965.1|DB962965
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
EST: gi|8827206|gb|BE210936.1|BE210936
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
EST: gi|151412093|gb|EV281905.1|EV281905
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAGTACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
EST: gi|192316740|gb|FK006443.1|FK006443
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
EST: gi|213591579|gb|DB955787.1|DB955787
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
EST: gi|213592188|gb|DB965979.1|DB965979
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCT
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCT
EST: gi|192316741|gb|FK006444.1|FK006444
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
EST: gi|16279667|gb|BI943554.1|BI943554
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
EST: gi|192317198|gb|FK007909.1|FK007909
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATGAAGACAAATGTGTTTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
EST: gi|19453064|gb|BM954474.1|BM954474
EST:     ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
EST: gi|192296657|gb|FG991225.1|FG991225
EST:     ATCTTGCATGCCCTGCCTCTCCGATTTTCTACAAATACAATCCAGTAAAG                         ACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG
genomic: ATCTTGCATGCCCTGCCTCTCCTATTTTCTACAAATACAATCCAGTAAAGgtatagtttg ... tactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttatctgaccctgaaagactatctaatttataatgaaacaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG
                       atctaat  putative branch site (score: 3)
                                            ttacttt  putative PPT
                      tatctaatttataatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagttatgtctagctactgctagtatcattggtcaataagttcatgtttatctgaccctgaaagactatctaatttataatgaaacaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG