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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgtttggtcgttctcttgataatctaggattaatcgtatatttttgtgattgttgagatttttattttcattcagtttgacgataattttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG

Basic information

species Glycine max
transcript GLYMA09G06890.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 6
ttatgtttggtcgtt--ctcttgataatctaggattaatcgtatatttttgtgattgttgagatttttattttcattcagtttgacga----taattttgt-tgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG
       ||| | ||  |   | |   | ||    |  |  | | |||   |  | | |   | ||| ||| |  ||    || |  |       |||||| || |||| || || ||||| ||||||||||| | ||||||||||||||| ||| | || ||| ||||||||||||
-------tggccatttgccacttactgtttatcgctgtttttttttttggtttgtagctataactttcattatttttggagttaattaactccttttttgtgtgtagGGGATAAAAGAAGGCTGGTATGATGGAGCAAGCATTGCTTTTGCTGTTCTCCTAGTTGTTGTTGTTACAG

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 7
---------------------ttatgtttggtcgttctcttgataatctaggattaatcgtatatttttgtgattgttgagattttt--attttcattcagtttgacgataattttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG
                      ||  |||||   ||| ||   |   |   || ||||   |  |     | |   |||   ||     || || | | | || ||  | |||  |    ||||||||||| ||||||||||||||||| ||||||||||| ||||| || |||||||| |||||||| || |
gtttgtgatgaaatcaattaactaaatttggctcttccctcttt--ccccagagtaatgtcacctccaaattaaccttggtcttacacaatctttactaacttggataacaatcat-cgacagGGTATCAAAGAAGGATGGTATGATGGAGGAAGCATTGCATTTGCTGTGATTCTTGTGATTGTTGTGACGG

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 8
-ttatgtttggtcgttctcttgataatctaggattaatcgtatatttttgtgattgttgagatttttattttcattcagtttgacgataattttgt----tgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG
 |    |   |  | | |||| |||||| | | | || | ||||| ||| | |||  |   ||||   |||| ||   | ||     | |||||||    |  ||||||| || |||||||||||||||||||| |||||||| |||||||||||||||||||| ||||||||||
atagaataatgatgct-tctttataatccatg-tgaaccatatatcttt-ttattagtttcatttgagtttttat--ggcttccattttattttgtcttctttagGGTATTAAAGAAGGATGGTATGATGGGGGGAGCATTGCCTTTGCAGTTATTCTTGTTATAGTTGTTACAG

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|207814735|gb|GD788980.1|GD788980
EST:     TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCCGAG                         GGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTG
genomic: TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCCGAGgtgaggtttg ... tttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTG
EST: gi|193357966|gb|FK318978.1|FK318978
EST:     TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCCGAG                         GGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATT
genomic: TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCCGAGgtgaggtttg ... tttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATT
EST: gi|208027309|gb|GD825777.1|GD825777
EST:     TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCCGAG                         GGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATT
genomic: TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCCGAGgtgaggtttg ... tttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATT
EST: gi|208094301|gb|GD894908.1|GD894908
EST:     TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCTGAG                         GGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATT
genomic: TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCCGAGgtgaggtttg ... tttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATT
EST: gi|207818770|gb|GD791585.1|GD791585
EST:     TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCCGAG                         GGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTG
genomic: TTTTAATGGTAGCTGCAGCGGCTTCATTGGCACTTGGGATAAAATCCGAGgtgaggtttg ... tttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgattgttgagatttttattttcattcagtttgacgataattttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG
                                gtttgac  putative branch site (score: 4)
                                            ttttgtt  putative PPT
               atttttattttcattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgtttggtcgttctcttgataatctaggattaatcgtatatttttgtgattgttgagatttttattttcattcagtttgacgataattttgttgcagGGTATCAAGGAAGGATGGTATGATGGGGGAAGCATTGCTTTTGCAGTTATTCTTGTTATTGTTGTTACAG

- atgtttg
- - - - - - - - - - - - - - - - - - - - - - ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgag