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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattaaacactcccaccatttcccacacggcaagaactcctcttttgatgttgaatattgaataaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA

Basic information

species Glycine max
transcript GLYMA03G33000.6
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
gtaaattaaacactcccaccatttcccacacggcaagaactcctcttttgatgttgaatattgaataaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA
                      | || || |  ||||  | | |  ||     |  |  |    ||    |  |  |  | |  |||  |||| |||  |||||||||||| ||||| ||||||||||||||||| |||||    |||||||| ||||||||||| || || || || || ||||||||||
----------------gtttggtccctactcaacaagtgcgctttcttcagaatgaatgaacagattctaaagtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA

upper sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
gtaaattaaacac-tcccaccatttcccacacggcaagaactcctcttttgatgttgaatattgaataaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA
     ||     | | ||| ||||| | |        ||| | || || ||||    |   ||  ||    ||    ||      |  | |||| |||  |||||| ||||| ||||| || |||||||||||||| |||||    ||||||||||||||||||||||| || || || || || |||||||
---gtttggcttcattccaacatttacaaagtccagcgaaatgctattctgatccccatgtttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA

upper sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 8
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaattaaacactcccaccatttcccacacggcaagaactcctcttttgatgttgaatattgaa--taaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA
     ||| | | ||     | ||  || |       |   | | |     |     | ||||||  ||    ||  ||  |||   ||  |||| |||||||| || ||||| ||||||||||| ||||| ||||| |||||||| |||||||| || ||||  |||||||| || |||||| | ||||| |
----gttagatattcaacgtacttgtcatatt-----agtacttataaaagtaacagagattgaaactagaagctctttctgcttgaat--agGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA

upper sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 6
gtaaattaaacactcccaccatttcccacacggcaagaactcctcttttgatgttgaatattgaataaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA
||| |  ||     |     || |  |      |||  ||| ||            ||  |||||| |    | |    | | | | | |||| ||||||||||| ||||||||||| || |||||||||||||| ||||| ||||| |||| ||||||||| ||||| ||||| || ||||| ||||| |
gtagaaaaagatgacaagatatatttcctctcccaattacttct-----------aaaccttgaattaatcttgaccttgatta-acacagGGAGAGAAAGATGACAAGATAATTGCAGTTTGTGCTGATGATCCTGAGTACCGACACTACACTGATATCAATGAGCTCCCTCCGCACCGTTTGGCTGAGA

upper sequence: GLYMA03G33000.6 (Glycine max), 3'ss of exon 8
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------gtaaattaaacactccc------accat-ttcccacacggcaagaactcc-tcttttgatgt-tgaatattgaataaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA
                              | |||  ||||   |        | ||| ||| || |  |   | ||    || |    | | || | ||  |||    | ||  ||    ||  |  |||| ||||| ||||| ||||| || |||||||||||||| ||||| |||||| |||| | ||| || ||||| ||| |||||||||||||  | || ||||
gtgagggactattatgccgtactctttgacggaaaccaaactagcttgtattgatcatgttctcatattgttcgtacctaatcatccactatatgtaaatctaatgttaaatt--tgtaaggacctgtagGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAA

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|193357096|gb|FK323568.1|FK323568
EST:     GTTGCTTTCTTCGGGCCAACGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAATTAGCTGTCTGTGCTGATGATCC
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATT-GCTGTCTGTGCTGATGATCC
EST: gi|151404690|gb|EV274504.1|EV274504
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
EST: gi|298199436|gb|HO042799.1|HO042799
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAACTGCTGTCTGTGCTGATG
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATG
EST: gi|7925031|gb|AW831057.1|AW831057
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAN                         GGGGAGAAAGATGATAAGATAATTGCTGTC
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTC
EST: gi|8827754|gb|BE211484.1|BE211484
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
EST: gi|192324459|gb|FK015810.1|FK015810
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
EST: gi|5510301|gb|AI856743.1|AI856743
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
EST: gi|10236851|gb|BE805739.1|BE805739
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
EST: gi|16105384|gb|BI893124.1|BI893124
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
EST: gi|192296495|gb|FG989111.1|FG989111
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
EST: gi|17022987|gb|BM094021.1|BM094021
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactcctcttttgatgttgaatattgaataaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA
                 ttgaatattgaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattaaacactcccaccatttcccacacggcaagaactcctcttttgatgttgaatattgaataaccacttattgcgctgatataaagGGGGAGAAAGATGATAAGATAATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA