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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctcttggtttcttttatgtgatgcaagttactcacagaatatttacctgaaatgttttgggttagatctaggtaaggtaaaggaaataatttcc...

Basic information

species Glycine max
transcript GLYMA10G34370.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G34370.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g01750.2 (Oryza sativa), 5'ss of exon 8
TCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctct-tggtttcttttatgtgatgcaagttactcacagaatatttacctgaaatgttttgggttagatctaggtaaggtaaaggaaataatttcc--------
||| |||||  |||||||| |  |||||    | ||    ||||| || |||||||||||||| || || ||||||||||| |||||||| |||||  | ||| || ||  |||| | || | | |       ||| | || |||||  |||  | | | |||| || ||| ||     ||  ||        |   |           
TCCTGCTGTGATTAGCAAACTGCACAAGCTTGTCAACCATAATGGTGGGGTAACATATATACACTGTACCGCTGGACTTGGGAGAGCTCCTGCTGTGACAgtaggtttccatggtcttttctttttt------gtttccca-agaattctta--taataggtttaggtttacattataatattgtcttcttctttcctgttcagttagt

upper sequence: GLYMA10G34370.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 8
TCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctcttggtttcttttatgtgatgcaagttactca---cagaatatt-tacctgaaatgttttgggttagatctaggtaaggtaaagga--aataatttcc
||| ||||| |||||||||||  ||||    || || |  ||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||| || |    |   |       | ||    ||| | ||   ||   |||| |  |  | ||   ||  ||| | |||||  |   |   |    | ||      
TCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttacatgccacccccccctaatttttgtttcccaagacaacttattgtttcacagattccttatgtttg-tctagagatccttttgcttcagtag-----

upper sequence: GLYMA10G34370.2 (Glycine max), 5'ss of exon 7
lower sequence: AT3G52180.1 (Arabidopsis thaliana), 5'ss of exon 7
TCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctcttggtttcttt--tatgtgatgcaagttactcacagaatatttac----ctgaaatgttttgggttagatctaggtaaggtaaaggaaataatttcc---------------------------------------------------------------------------------------
|||||| || ||| | |   | ||||| ||  | ||    |||||||| || |||||| | || |||||||||||| | ||||| ||||| |||||||||||||||  |         ||  || |   | |   ||   | |    | ||| |     |||||   | |  |   | |  |   |  |||   |   ||||||                                                                                         
TCCAGCCGTGGTTGGTACTCTTTACAAAGCTGTTAAGCGAAATGGAGGAGTTACATATGTGCACTGCACTGCTGGAATGGGAAGGGCTCCTGCTGTTGCGgtatgttacagaaacctgttactaagctcttctctttttcccccttttctttccagtattgaaaaaatgtaagactgttgcaaaca--gtagttgtcttaattttgtgcttatttggttgactcatgaaggtatgaacaagttttcacattttgctgactgatactgagaagggatattaatttcattttcag

upper sequence: GLYMA10G34370.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 5'ss of exon 8
TCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctcttggtttcttttatgtgatgcaagttact----cacagaatatttacctgaaatgttttgggttagatctaggtaaggtaaaggaaataatttcc
||||||||| || ||||||||||||||||| ||||||   ||||||||||| || |||||||| ||||| ||||||||||| |||||||| || || ||||||||  |||   |||  | |  |  ||   | ||| |    |  |     |||| || | |  |   |  ||  |  ||  |     |     |   | |   
TCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttctccattttgtctcagaaatatgaattaattctgcctaaggcttttagctaagaaatac-gaattgtaattaaatggcacacttctacggaat---

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|22524300|gb|BU083111.1|BU083111
EST:     ACTTGGAAGAGCTCCAGCTGTTGCG                         TTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACGAGGCTCATACA
genomic: ACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctct ... tttgtctcagTTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACGAGGCTCATACA
EST: gi|192322536|gb|FK014657.1|FK014657
EST:     TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCG                         TTGGCTAATATGTTTTGG-TTCTGGGTTATAAACTTAACGAG-CTCATACA
genomic: TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctct ... tttgtctcagTTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACGAGGCTCATACA
EST: gi|22524365|gb|BU083176.1|BU083176
EST:     ACTTGGAAGAGCTCCAGCTGTTGCG                         TTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACGAGGCTCATACA
genomic: ACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctct ... tttgtctcagTTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACGAGGCTCATACA
EST: gi|9899914|gb|BE608882.1|BE608882
EST:     TAACATATATACATGGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCG                         TTGGCTTATATGTTTTGGGTTTTGGGTTATAAACTTAACGAGGCTCATACA
genomic: TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctct ... tttgtctcagTTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACGAGGCTCATACA
EST: gi|9564018|gb|BE473527.1|BE473527
EST:     TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCG                         TTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACGAGGCTCATACA
genomic: TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctct ... tttgtctcagTTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACGAGGCTCATACA
EST: gi|120532166|gb|EH260299.1|EH260299
EST:     TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCG                         TTGGCTTATATGTTTCGGGT
genomic: TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctct ... tttgtctcagTTGGCTTATATGTTTTGGGT
EST: gi|193710242|gb|FK642940.1|FK642940
EST:     TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCG                         TTGGCTTATATGTTTTGGGTTTTGGGTTATAAACTTAACG
genomic: TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctct ... tttgtctcagTTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACG
EST: gi|6916528|gb|AW398058.1|AW398058
EST:     TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCG                         TTGGCTTATATGTTNTGGGTTTTGGGTTATAAACTTAACGAGGCTCATACA
genomic: TAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctct ... tttgtctcagTTGGCTTATATGTTTTGGGTTCTGGGTTATAAACTTAACGAGGCTCATACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctcttggtttcttttatgtgatgcaagttactcacagaatatttacctgaaatgttttgggttagatctaggtaaggtaaaggaaataatttcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT