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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcttcaagtgacaattagtttgaaggtgtagtattgtttcttatcttaaactgctcatgtaggaggcatatatttgatgcttgattgtcttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAAT

Basic information

species Glycine max
transcript GLYMA08G47790.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G47790.3 (Glycine max), 3'ss of exon 1
lower sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------------------------------------------------gctcttcaagtgacaattagtttgaaggtgtagtattgtttcttatcttaaactgctcatgtaggaggcatatatttgatgcttgattgtcttcatt-cagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAAT
                                                                                                    |||  |||| ||| ||  ||  ||| || | ||         |   ||     |   | | |  || | |  | ||||  ||  |||| |   || |||  | |  || ||     | | ||| ||||||| | ||| |||||| ||    ||||||||||| |||||||| ||||| |||||||| ||||||||||||
gtaagtctttatatccatttgatgcatgtcttttgtctctgtttctcgctcttggggttcaccaaaaattgaatctttttagctggaaacgtaccacgaatctcaaagtaacatttt-ttataagatggattaggaaaagcaactgtatttcccctttttggttggtaaaagtctgattttt--ttgtttaatttgcagTGTGAGGTGTTCAGTGTCTGGTGGAAATGGAACTGCTGGAAAGAGAACGACTCTTCATGATCTATATGAGAAGGAAGGTCAGAGTCCTTGGTATGATAAT

upper sequence: GLYMA08G47790.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 1
--gctcttcaagtgacaattagtttgaaggtgtagtattgtttcttatcttaaactgctcatgtaggaggcatatatttgatgcttgattgtcttcatt-cagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAAT
  | | ||  | |      || ||  || || || | ||   |     |||   ||| |  |  ||   |   |  | | || |   ||  | || ||| |||  ||| ||| ||||||   || || |||||||| |    |||||| |||   ||||||||||| |||||| | | ||||||||| |||||||||||||| 
ttgttgtttcatttttctctaattctaaagtttaatttt---taaaggctttctctgattgtaaagtttgagaagttctcattccgtatgttatttattacagTGTCAGATGTTCCCAACTTGAGGGAAATGGAAGCCAAATAAAGAGAACAACTCTTCATGATCTCTATGAGCAGGGAGGGCAGAGCCCATGGTATGATAAC
















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|151412865|gb|EV282677.1|EV282677
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|17153408|gb|BM143341.1|BM143341
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|213587880|gb|DB959704.1|DB959704
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|26059043|gb|CA801957.1|CA801957
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|6481766|gb|AW201037.1|AW201037
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|213591047|gb|DB973788.1|DB973788
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|254315550|gb|GR825359.1|GR825359
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|6133795|gb|AW132188.1|AW132188
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACCGG
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGA-CAG
EST: gi|19453272|gb|BM954682.1|BM954682
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|9439831|gb|BE440344.1|BE440344
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|254346140|gb|GR859753.1|GR859753
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|254336110|gb|GR841435.1|GR841435
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|5126502|gb|AI748238.1|AI748238
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|16106060|gb|BI893800.1|BI893800
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGTTATTGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|15813619|gb|BI785894.1|BI785894
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACATT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|9565717|gb|BE475226.1|BE475226
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|11688467|gb|BF596143.1|BF596143
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|18039782|gb|BM308076.1|BM308076
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|19936998|gb|BQ081103.1|BQ081103
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|41146374|gb|CK606585.1|CK606585
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|192309107|gb|FG999390.1|FG999390
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|16347482|gb|BI973077.1|BI973077
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|209710574|gb|BW676526.1|BW676526
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|209718567|gb|BW662685.1|BW662685
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|254326716|gb|GR832868.1|GR832868
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|16996699|gb|BM086071.1|BM086071
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|17022331|gb|BM093365.1|BM093365
EST:     CTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: CTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|254322565|gb|GR837979.1|GR837979
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT
EST: gi|22540587|gb|BU090430.1|BU090430
EST:     TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCG                         GATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGG
genomic: TCCGCTTCCCTCCGATCCATTCACTCCCTCCCTCTTAAAACCTCCTTGCGgtaagttttc ... cttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaaactgctcatgtaggaggcatatatttgatgcttgattgtcttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAAT
                                   gcttgat  putative branch site (score: 5)
                                            tcttcattc  putative PPT
                        atatatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctcttcaagtgacaattagtttgaaggtgtagtattgtttcttatcttaaactgctcatgtaggaggcatatatttgatgcttgattgtcttcattcagGATCAAATGCTCCCAAACAGATGGGAATGGAAGTCCTGCAAAGAGGACAGTGCTTCATGATCTTTATGAGAAAGAAGGGCAGAGTCCATGGTATGATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
-ctcttca
- - - - - - - - - - - - - ggtgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct