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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT

Basic information

species Glycine max
transcript GLYMA06G05890.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
------acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagtattgaa--------tcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
      || || | ||    ||   ||    ||||  ||  | |     | |||     ||||| |||  | |   |||   | | |||||        |||| ||||||||||||||||||||| || || |||||||| ||||| ||||| || ||||  || ||| || |||| ||||||||||||||||| ||  ||
ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaaca-----gttgaatat--gttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT

upper sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagtattgaa--------tcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
 | || | ||    ||   ||    ||||  ||  | |     | |||     ||||| |||  | |   |||   | | |||||        |||| ||||||||||||||||||||| || || |||||||| ||||| ||||| || ||||  || ||| || |||| ||||||||||||||||| ||  ||
-cttcctaccgcattacttgaactgatttggtgattgatgaattaaca-----gttgaatat--gttttgcataataatgttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT

upper sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------acctcttgcctttgtaaaagatgctatttattgtcttaacttcttaca---ttcttgttgagta-taagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
                    |         | |||| |  |  |||||   |  ||| | | ||   | |   || | || |||  | || ||       |    || ||||| |||||||||||||| ||||| || ||||| || || |||||| |||| ||||  |||| | |||| ||||||| |||||||||||||||  | 
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG

upper sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
-acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagt-attgaatcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
 |   ||   | |||||     || |    |||    ||  ||   |  |  || ||||   |||  |  ||| |   |  ||||  | |||||| ||||||||||||||||||||||| ||||| || ||||||||||| || || ||||| |||||   ||||||||||||||||||| ||||  | 
cattactcttccttgtattcattggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattg--ttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA

upper sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35201 (Selaginella moellendorffii), 3'ss of exon 4
acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
                                                  ||| | ||  |     |||  |   ||   || ||  || | | |  ||||| ||||| ||||| |||||  | |||||||||||| ||||||||   ||| | ||||||||||| ||||||||| |   ||| || 
---------------------------------------------gtgagcttatagatcag----tccgtaaacgaa-gttaaa--ttctggtactcagGTAATGCTACTTGGGTTCGTTTTGCTGGGACGTTCTTTGGAGGAACGTGCACGCATTCAGGCATCCAGCGATATGCAGAGACTCCTG

upper sequence: GLYMA06G05890.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ24140 (Selaginella moellendorffii), 3'ss of exon 4
acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
                                               |  ||| | ||  |     |||  |   ||   || ||  || | | |  ||||| ||||| ||||| |||||  | |||||||||||| ||||||||   ||| | ||||||||||| ||||||||| |   ||| || 
---------------------------------------------gtaagcttatagatcag----tccgtaaacgaa-gttaaa--ttctggtactcagGTAATGCTACTTGGGTTCGTTTTGCTGGGACGTTCTTTGGAGGAACGTGCACGCATTCAGGCATCCAGCGATATGCAGAGACTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattcttgttgagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
 ttcttac  putative branch site (score: 2)
                                        tctttt  putative PPT
                                 tattgaatctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acctcttgcctttgtaaaagatgctatttattgtcttaacttcttacattcttgttgagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTCGTGCTTCTGGGACGTTCTCTGGAGGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- ctcttgc
- - - - - - - - - -gatgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctca