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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaatattacaacatgataaataattgaagtttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

Basic information

species Glycine max
transcript GLYMA06G24520.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaatattacaacatgataaataattgaagttt--gctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
 |    |||  | |    ||  |  |  | |  |  |  |     |  | | | |   ||||||  |  |   ||||||   || |  | ||   | |  || ||||  ||   ||| | |||||| |||||||||||||||||||| ||||||||||||||||| ||||  || || || || ||||||||||||||    
atgttatgggcatgcttccagcactttaaactcat-gtcttgttctatattttgatttcatgatgcactacataagttttgacttgctttatgacttt-tagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG

upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaa-gatggaatattacaacatgataaataattgaagtttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
 ||        |   | | |     |          |  |    | |    |||       |     ||||  ||| |||     |   ||     | ||||||||  ||   ||| || || || ||||| |||||||||||||| ||||||||||||||||| || |  || ||  | || ||||||||||| ||    
-tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatgcatgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG

upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------------------------ttacggtggttaagaaa-acaaaaaatccagcgaagaggataaagatggaatattac-aacatgataaataattgaagt-ttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
                                                                                             |  |  ||  ||  |   || |  | |     | |    ||||      | |||| |  || || |  |||    |  |  ||     || | | |    ||||||||  || ||||||||||||||||||||||| ||||||||||| ||||||||||||||||| || |  || |  || ||||||| |||||||||    
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG

upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: AC217311.3_FGT007 (Zea mays), 3'ss of exon 1
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaatattacaacatgataaataattgaagtttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
                                            ||| | | || ||   | | |        |  |||  ||  |  |||  | ||||| |||| |||   ||| || ||||| |||||||||||||| ||||| |||||||| |||||||| || |  |||||  | |||||||||||||||||    
------------------------------------------gtatgcattcttccatgttcacagc------atctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 7
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaatattacaacatgataaataattgaagt-ttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
| || |    | ||  |  | | || | |    |    ||||  |     | ||      |  |  ||  |   ||  |   ||  |  |||  | ||||| |||| |||   ||| || ||||| |||||||||||||| ||||| |||||||| |||||||| || |  |||||  | |||||||||||||||||    
tgacagactgttagggataacacaacctatgacaatttataataactacgt-ttgtcctttcttccatgttcacagcatctttaataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G008647_T02 (Zea mays), 3'ss of exon 4
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaatattacaacatgataaataattgaag----tttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
   |    |       || || | | | |    |    ||||  |     | ||      |  |  ||  |   ||    |||  ||  |  |||  | ||||| |||| |||   | | || ||||| |||||||||||||| ||||| |||||||| |||||||| || |  |||||  | |||||||||||||||||    
---caaaagcatctttaataatatacctatgacaatttataataactatgt-ttgtcctttcttccatgttcacagcatctttaataataatatacctctgcagATATGGTGTTTCTAGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G110742_T02 (Zea mays), 3'ss of exon 7
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaatattacaacatgataaataattgaagtttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
                                            ||| | | || ||   | | ||       |  |||  ||  |  |||  | ||||| |||| |||   ||| || ||||| |||||||||||||| ||||| |||||||| |||||||| || |  |||||  | |||||||||||||||||    
------------------------------------------gtatgcattcttccatgttcacaac------atctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G404011_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------------------------ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaa-tattacaacatgataaata---at-----tgaagtttgctagaataatat--ttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
                                                                                   || || | ||  ||  | ||||| | |  |    |  | | |  ||    | |       ||| | |||   ||       |  | |   | ||||||||   | ||||| |||| |||   ||| || ||||| |||||||||||||| ||||| |||||||  |||||||| || |  |||||  | |||||||||||||||||    
gtatgcattctgacttgtctatttcagtggttgttatgcacattagctttcagcctttagtttaacaccattggattttcttatatggcgattgtgatga-aaaaatttcctcaggaatcacagaagtgattctctcgtcgtttgacagatatggatgttcacaacatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGTCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G170845_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------------------------ttacggtggttaagaaaacaaaaaatcc--agcgaagaggataaagatggaatattacaacatg-ataaataattgaag----tttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
                                                                                     ||||| | || | ||||| |     ||   |   |      | |   |    |  |   |||   ||  ||  |   ||    |||  ||  |  |||  | ||||| |||| |||   ||| || ||||| ||||||||||  || ||||| |||||||| |||||||| || |  |||||  | |||||||||||||||||    
gtatgcattctgacttgtctatttcagtggttgttatgcacattagctttcagcctttagtttaacaccactggattttcttatattacgattgtgatgaaaaaatttcctcatgaatcacagaagtgattctctcgtcgtttgacagatatggatgttcacagcatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTATCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
ttacggtggttaagaaaacaaaaaat-ccagcgaagaggataaagatggaatat-tacaacatgataaataattgaagtttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
 || | |||  | | |    |  ||| ||         | | ||  |    ||| |   | |  |  || |  | |||        | ||   | ||| ||| ||||  ||||||||||| || || ||||| ||||||||||||| ||||||||||||| | || || |  ||||| || || || |||||||||||    
gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagac-----aagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC

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|193530804|gb|FK487003.1|FK487003
EST:     ATTGCAAATCTGGATGCTGATAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: ATTGCAAACCTGGATGCTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|193328670|gb|FK294802.1|FK294802
EST:     GTAGTAATTGCAAATCTGGATGCTGATAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: GTAGTAATTGCAAACCTGGATGCTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|208248956|gb|GE046385.1|GE046385
EST:     ATGCTGATAAATATAGGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: ATGCTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|193677036|gb|FK618774.1|FK618774
EST:     ATTGCAAATCTGGATGCTGATAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: ATTGCAAACCTGGATGCTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|208064941|gb|GD861639.1|GD861639
EST:     GTAGTAATTGCAAATCTGGATGCTGATAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: GTAGTAATTGCAAACCTGGATGCTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|208132923|gb|GD931626.1|GD931626
EST:     GTAGTAATTGCAAATCTGGATGCTGATAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: GTAGTAATTGCAAACCTGGATGCTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|207825604|gb|GD800955.1|GD800955
EST:     CTGATAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: CTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|208095879|gb|GD894163.1|GD894163
EST:     CTGGATGCTGATAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: CTGGATGCTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|208323036|gb|GE118275.1|GE118275
EST:     TAGTAATTGCAAATCTGGATGCTGATAAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: TAGTAATTGCAAACCTGGATGCTGAT-AAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|193357852|gb|FK320614.1|FK320614
EST:     GTAGTAATTGCAAATCTGGATGCTGATAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGGAACAA
genomic: GTAGTAATTGCAAACCTGGATGCTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
EST: gi|193414440|gb|FK377440.1|FK377440
EST:     GTAGTAATTGCAAATCTGGATGCTGATAAATATAAGGATCTGGCTGAAAA                         GTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA
genomic: GTAGTAATTGCAAACCTGGATGCTGATAAATATAAGGATCTAGCTGAAAAgtgagtttta ... atttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaatattacaacatgataaataattgaagtttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT
                 ataaataattgaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaatattacaacatgataaataattgaagtttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - ggtggtt
- - - - - -aagaaaa
- - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctag