Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgcattgatacttacaacaaatcatttcttctgaatttagatttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT

Basic information

species Glycine max
transcript GLYMA15G04670.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G55280.1 (Arabidopsis thaliana), 3'ss of exon 3
gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgcattgatacttacaacaaatcatttcttctgaatttagatttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT
                    |||||  |||  |  |   | |   ||  || ||    |||   | | ||       || | ||  ||| | ||   ||||||||| || || |||||||| ||||| |||||||| ||||||||||| ||  |||||||||| ||||| || || || |||||| || ||   || |  
------------------gtaaacactaaaacttcactgaga-tatgggtttatgtaaacatggagtgat-------gagtgtatgtttgtatg---cagGCCCGATGGAACAAAGAAGGCGTATGTGAGGTTGACTCCTGATTATGATGCTTTGGATGTGGCTAACAAAATCGGGATCATCTAATCTGATCATTGTCGC

upper sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04090.t01 (Vitis vinifera), 3'ss of exon 3
gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgcattgatacttacaacaaat-----catttcttctgaatttagatttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT
      | |      |||   ||  |  ||| |       ||   ||   |  | ||   ||  | |     ||  ||||||||  ||| |||||| || | |||||| || || ||||||||||| ||||| |||||||| || || ||||| ||| |||||||||||||||| ||||| || ||||||  ||    ||| |  
----ttagattggataaacttaattatgaatatcctgagcaagaatgttcttttgctgggaaatattttcgacaactcttctgacatta-atttttgtgatccagGCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGCCTTGGATGTGGCCAACAAAATTGGGATCATCTAAGGTAGGATCTGTCTA

upper sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgca--ttgatacttacaacaaatcatttcttctgaatttagat-ttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT
       | | ||  | ||  | | |     | || |       || ||  || |||| |     ||||  | |  | |  ||     | | || | || |||||| || || || ||||| || ||||| |||||||| || |||||||| ||  |||||||||| ||||||||||| ||||| |||| || |  |      
---tttcttatatatatatatatcgagttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA----

upper sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g00250.t01 (Vitis vinifera), 3'ss of exon 3
---gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgcattgatacttacaacaaatcatttcttctgaatttagatttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT-
     ||   | | ||         | | ||| |  | || |   |  ||   |  |  ||   | || | || |   || |  ||  || ||| ||||||||||| || || ||||||||||||||||| ||||||||||| || ||||| ||| |||||||||| |||||||| || || |||||||   ||   || | | 
cagaatggtgtgatatatgggcatcataccaagt--ggattagcgatgtggcatagtggttgtca-aattgatatgaactaaccttctatctttgtgttgcagGCCTGATGGAACCAAGAAGGCTTATGTTAGGTTGACACCGGACTATGATGCCTTGGATGTGGCAAACAAGATCGGGATCATCTAAATCTATAT-TGCCTTT

upper sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S459_11V6.1 (Physcomitrella patens), 3'ss of exon 1
gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgcattgatacttacaacaaatcatttcttctgaatttagatttttctgttg---cagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT
  |    |    ||   ||     |   | ||  ||| |     |  ||||  |   ||  |      ||||||  ||   | | |||| ||| ||    |||||| || ||  ||||||||||||| || ||  ||||| | |||||||| || || ||||||||||||||||| || || || |||| |   |  |    |
--taattttttttg-ggatttcgtattgatttgatatcacctgttcccattcctctctaggatgtgaaatttctaatgtggtcaaatttatctattttctcagGCCTGATGGAGCCAAGAAGGCTTACGTGAGACTGACAGCAGATTATGATGCGCTTGATGTGGCCAACAAGATCGGTATCATATAAATTTTCTGTTCAATT

upper sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S146_96V6.1 (Physcomitrella patens), 3'ss of exon 1
gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgcattgatacttacaacaaatcatttcttctga-atttagatttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTA-ATTCCTGGCCT
|| |  |    | ||   |     |  |||  ||  || ||  | |   | |    | |   |  |||       ||||  | |    |||| |    ||| || || ||  | |||||||||||||| ||||||||  | ||||| ||||| || ||||| |||||||||||||| || || || | |  ||| ||     
gtagttactg-acgctcgtctggtaggaaaactgggtgcaatgcgtaagtcgccgttcaattctcatctacgtggctgacgtatcctgtttttttccccagACCTGATGGAGCGAAGAAGGCTTATGTGAGGTTGACGGCAGATTACGACGCTCTTGATGTTGCCAACAAGATTGGCATCATTTAGATTGCATTGCTCTTA-

upper sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S47_274V6.1 (Physcomitrella patens), 3'ss of exon 1
gttgccataacatgcaaatgaaacaacaaatttgtatgaaaa--acttgcattgatacttacaacaaatc----atttcttctgaatttagatttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT
      | | || |  |||||   |   |||  |  |  ||   |||||    |    | | |    |||    ||||| | ||  | |  |  | | | ||  ||||| || ||  | |||||||| ||||| || |||||| ||||||| || || || |||||||||||||||||||| || ||||||| |   |  |    |
-----gaaatcacggcaatgattgagttaatcagagtccaatttacttgttccggaggtgaaactccatccctgatttcctatgtgtctcaacatgttt-ttctagGCCTGATGGAGCTAAGAAGGCGTATGTGAGATTGACAGCTGATTACGATGCGCTTGATGTGGCCAACAAGATTGGTATCATCTAAATTTTCTGTTCAATT

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|209725405|gb|BW651549.1|BW651549
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATAATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|8404081|gb|BE059715.1|BE059715
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCANGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|213607965|gb|DB963023.1|DB963023
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|298178914|gb|HO024649.1|HO024649
EST:     GTCAAGAAGATGTATGATATTCGGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|6071966|gb|AW101353.1|AW101353
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGANCG
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGA-CG
EST: gi|298179054|gb|HO024789.1|HO024789
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|10231523|gb|BE800411.1|BE800411
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|14126262|gb|BG790700.1|BG790700
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|213611697|gb|DB969085.1|DB969085
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|209712413|gb|BW671265.1|BW671265
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|7685908|gb|AW756556.1|AW756556
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|31462027|gb|CD404055.1|CD404055
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGN
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACG-
EST: gi|12496334|gb|BG047012.1|BG047012
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|209723033|gb|BW668879.1|BW668879
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|213619677|gb|DB965623.1|DB965623
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|192313125|gb|FK004701.1|FK004701
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|192313126|gb|FK004702.1|FK004702
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|213593833|gb|DB957953.1|DB957953
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|8404100|gb|BE059734.1|BE059734
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|20497965|gb|BQ272895.1|BQ272895
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAATGCTTATGTCAGGATGACACCCGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|7686389|gb|AW757037.1|AW757037
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
EST: gi|298166750|gb|HO010189.1|HO010189
EST:     GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAG                         GCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC
genomic: GTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtgagtcttt ... tctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcattgatacttacaacaaatcatttcttctgaatttagatttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT
        tacttac  putative branch site (score: 1)
                                         tttttctgtt  putative PPT
                               tgaatttagattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgcattgatacttacaacaaatcatttcttctgaatttagatttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT

gttgcca
- - - - -acatgca
- - - - - - - - - - -aacaaca
- - - - - - - - - - - - - - - - tgtatga
- - - - - - - - - - - - - - - - - - - - - -cttgcat