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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactttcagaaaataaatattattgtttttggttctatttattttttgaattaatatgatcattatgatgtcataacctttgtacccattggttaagtaatttgtcattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

Basic information

species Glycine max
transcript GLYMA19G37570.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os09g39320.1 (Oryza sativa), 3'ss of exon 11
gtaaactttcagaaaataaatattattgtttttggttctatttattttttgaattaatatgatcattatgatgtcataacctttgtacccattggttaagtaatttgtcattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
       ||     |    ||||| |  ||||||   || ||   |   ||  || | |||| | ||    |  || |||     | |  | |  ||||||||| | |  ||    |   ||||| ||||||||||| ||||| |||||||| |  ||||| ||||||||| | ||| |||| |||||||| ||||| ||||||||||| ||||| ||||| 
----gtattgtattatctcatattctcttttttgtgacttttgtctacctgctttcacatgaacttttaactcccaaaacaagaattcatactatttaagtaatctctggttgc--ttgacagGCAAAGGGAATGAACTATCTACATAAACGTAGCCCTCCTATTGTTCATCGTGATTTGAAGTCTCCAAATCTTCTAGTTGACAAGAAGTATACCGTGAAA

upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
------------------gtaaactttcagaaaataaatattattgttt--ttggttctatttattttttgaattaatatgatcattatgatgtcataacctttg-tacccattggttaagt------aatttgt-cattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
                   |     | |||||  ||  | | |  |  |   |||   |||   || | | || ||| | | | |   |    ||| ||   | | | |   ||  | ||        | |||||  |  ||| | | ||||||||||| |||||||| ||||| || ||||||||||| || || ||  | ||||| || || ||||| ||  | ||||| || || || || ||||||
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaa-aggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatcattgattttgtgtaccttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG

upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 11
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaactttcagaaaataaatattattgtttttggttctatttattttttgaattaatatgatcattatgatgtcataacctttgtacccattggttaagtaatttgtcattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
                          | | |||  |||  | | ||   || ||   |  ||| | |      || |    ||| | | ||| |   |  |  |||   ||| ||     |||||||||||||||||||||||||| || ||||||||||| ||||| ||||||||||| |||||||||||| |  | |||||||| ||||||||||| |||
-------------------------gtatgtttaattccttatgttacatgtatgggt--gattacttcctgatcttggtgtttcttcacatgga--actttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG

upper sequence: GLYMA19G37570.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 10
gtaaactttcagaaaataaatattattgtttttggttctatttattttttgaattaatatgatcattatgatgtcataacctttgtacccattggttaagtaatttgtcattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
 ||   ||| ||    | | | |||||     ||| |  |    ||||   |  ||| || |   || |  | | || |  |  || |   ||          ||| |  ||   |    ||||| ||||| ||||||||||||||||||||||||||||||||||||||| ||||| |||| |||||||||||| | |||||||| ||||| || ||||||
-tatttttttag----tgattgttatt-----tggatgcacc--ttttaccagctaaaataac--ttgttttattatcatttccgtgctttttt---------tttttttttaaaacaaacagGCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAG

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|208031806|gb|GD829494.1|GD829494
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|298178752|gb|HO024487.1|HO024487
EST:     CTACAGAGATGTTGGGTGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|208211092|gb|GE012153.1|GE012153
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAAATTATCTTACATAAACGCAATC
genomic: CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAA-TTATCTT-CATAAACGCAATC
EST: gi|193637696|gb|FK583543.1|FK583543
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|208307044|gb|GE101556.1|GE101556
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCAATAAACGCAATCCTC
genomic: CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAATTATCTTCA-TAAACGCAATCCTC
EST: gi|193369249|gb|FK337113.1|FK337113
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCA
genomic: CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCA
EST: gi|208289273|gb|GE084978.1|GE084978
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTACATAG
genomic: CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTT-CATAG
EST: gi|207701046|gb|GD681787.1|GD681787
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|207770421|gb|GD742833.1|GD742833
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|207701641|gb|GD681864.1|GD681864
EST:     ACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGTATTGTG                         GCTAAGGGAATGAAATTATCTTCAT
genomic: ACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATG-AT-GTGgtaaactttc ... tcatgtgcagGCTAAGGGAATGAA-TTATCTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgtcataacctttgtacccattggttaagtaatttgtcattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
     tcataac  putative branch site (score: 2)
                                       tcattttc  putative PPT
                                taatttgtcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactttcagaaaataaatattattgtttttggttctatttattttttgaattaatatgatcattatgatgtcataacctttgtacccattggttaagtaatttgtcattttcatgtgcagGCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA