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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatggaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA

Basic information

species Glycine max
transcript GLYMA02G45430.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
------ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatggaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
      ||  |||  | ||  ||   || || | |    |  | ||     |      ||| ||      |       |||   | ||| |      | | ||||||||||||||| |||||| |||||||| || || |||||||||||| |||| |||||||| || ||||| |||||||| |||||||||||||| || || |
tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgag---taattctc---attaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA

upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g03130.t01 (Vitis vinifera), 3'ss of exon 3
ttaggaaagaaatactagaaca--aatat-ttgtattctaggttccaattgcagtcttattggacaatgaacatgg--aggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
     || |  |  || | |    ||||| |||||||  |  |||  |||  |     ||     | |   | |    | ||||   |  |     |   ||||||||||||||| ||| || ||||  || ||||| ||||| |||||| |||||||||| ||||| ||||| |||||||| ||||||||||||||||| || |
-----aatgtcaagcttgtattttaatatgttgtattgcaccttctgattaaaaaaaaatgtcgtatttcccctcattatgtttagctactacatgtcgctgcagATTTTTGAGAAGAACCCAACCACAATCAAGAACTATGGGATTTGGTTGCGGTATCAAAGTCGAACTGGTTATCACAACATGTACAAGGAATACCGTGACA

upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g03150.t01 (Vitis vinifera), 3'ss of exon 3
ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatggaggtttgattttttgtgctg------attgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
         |  | |||   |||     ||||||     |||  |||| |          | | |    || |   ||   | | ||  ||||      | ||||||||||||||| ||| || ||||  || ||||||||||| ||||||||||||||||| ||||| ||||| |||||||| ||||||||||||||||| || |
------tcaagcttctacttcaatatgctgtattggcccttctgattgtaaagggggaaaaaactttgtattgcccttcattatgtttagctgcatgtcactgcagATTTTTGAGAAGAACCCAACCACAATCAAGAATTATGGGATTTGGCTGCGGTATCAAAGTCGAACTGGTTATCACAACATGTACAAGGAATACCGTGACA

upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S74_193V6.2 (Physcomitrella patens), 3'ss of exon 3
------------------ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatggaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
                  | ||   | |    || |||   ||     | | |  |     |   ||||    | | | |  |||| ||| |  | |||      || |    ||||||||||||||| | | |||||||  || ||||| ||||| || ||| |||| ||||||||||| || ||||| ||||| ||||||||||            
ttcaatttcgaaccgttctcagtgtatacgctcttgaaaccatcccaatgt-cgggaaattataagcagagacaattgtcgttgaatatgaa--tctgaccagACGTTC---CTGCAGATTTTTGAGAAGTACCCTACCACTATCAAGAACTATGGTATCTGGGTGCGTTATCAGAGTCGGACCGGGTACCACAACATGTACAAGG------------

upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S44_13V6.1 (Physcomitrella patens), 3'ss of exon 3
ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtc-ttattggacaatgaacatggaggtttgatt------ttttgt-gctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
    || | |    | |   ||  | |   ||  |||       |  ||| |  |||  | |   || |||| |  || | | |      |  ||| ||  ||| ||||||||||||| | | |||||||  || ||||| || || |||||| || ||||||| |||||||| || || ||||| ||||||||||||||||| ||| 
----gacaaacgggcaatgccacgtttcgttaacctaaa----gagagcattggttaccgaaggttgcacatcggtgtgtcactgaacactcctgttgcccattccagATTTTTGAGAAGTACCCTACCACCATCAAGAACTACGGTATTTGGGTGAGGTATCAAAGTCGTACCGGATACCACAACATGTACAAGGAATACCGTGATC

upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 3
ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatggaggtttgattttttgtgctgattg--------cagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
      |   | |  | ||      | || | ||     |   |||    | |||    || | |||   |     ||  |||  |  ||  | ||         ||||||||||||| | |||| ||||  || ||||| ||||| || ||| |||| |||||||| || ||||| || ||||| ||||||||||| ||||| ||  
----agatacattgtttgagggcgaaattatgttaacaatgttaatcatgggctt----gaaagtgacgttacgaattctattactaatgtagtttttgaaccttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGTTATCAGAGCCGGACTGGCTACCACAACATGTACAAGGAGTACCGTGACC

upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S74_193V6.1 (Physcomitrella patens), 3'ss of exon 3
------ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatggaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
      | ||   | |    || |||   ||     | | |  |     |   ||||    | | | |  |||| ||| |  | |||      || |    ||||||||||||||| | | |||||||  || ||||| ||||| || ||| |||| ||||||||||| || ||||| ||||| ||||||||||| || || ||  
ccgttctcagtgtatacgctcttgaaaccatcccaatgt-cgggaaattataagcagagacaattgtcgttgaatatgaa--tctgaccagacgttc---ctgcagATTTTTGAGAAGTACCCTACCACTATCAAGAACTATGGTATCTGGGTGCGTTATCAGAGTCGGACCGGGTACCACAACATGTACAAGGAGTATCGTGACC

upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S5_178V6.1 (Physcomitrella patens), 3'ss of exon 3
ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggac--aatgaacatggaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
  |  |     ||| |  |    | | |  |           |   || ||    | ||  |   || | ||||    |           |  |  || ||||||||||||| | | |||||||  || ||||||||||| || ||| |||| ||||||||||| ||||| || ||||| ||||||||||| ||||| ||  
--atcactagcatattttatgggagactcattcagcgacaaacggatgtagaggaaatgagccagataatcatgatactgaatgacccaatcgttgtttcagATTTTTGAGAAGTACCCTACCACTATCAAGAATTATGGTATCTGGGTGCGTTATCAGAGTCGAACTGGCTACCACAACATGTACAAGGAGTACCGTGACC

upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ38689 (Selaginella moellendorffii), 3'ss of exon 3
ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatg-gaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
                           |    ||||   ||    || |  | || | |  |  |  |  || ||  ||||    || |||       |||||||| |||| ||| || |||| ||| ||||| ||||| || ||| || |||| ||||| || || ||||| ||||| ||||||||||| ||||| || |
--------------------------gtaaagttctttctttttctttc--ttttctcgagccttacaagtgagaactttggaacttcgtgaca----cagATTTTCGAGAAGAACCCGACCACGATCAAGAACTATGGCATCTGGGTGAGGTACCAGAGCCGGACGGGGTACCACAACATGTACAAGGAGTACCGCGACA

upper sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ31458 (Selaginella moellendorffii), 3'ss of exon 3
ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatggaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
                     |||  | | | || |   |||      |  |  | | |    |  |     ||  ||||    || |||       |||||||| |||| ||| || |||| ||| ||||| ||||| || ||| || |||| ||||| || || ||||| ||||| ||||||||||| ||||| || |
-------------------gtaaagttctttctttttctttctttcctcgatgctctagccttacaagtg-agaactttggaacttcgtgaca----cagATTTTCGAGAAGAACCCGACCACGATCAAGAACTATGGCATCTGGGTGAGGTACCAGAGCCGGACGGGGTACCACAACATGTACAAGGAGTACCGCGACA

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|10846378|gb|BF069287.1|BF069287
EST:     GCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: GCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|298196038|gb|HO044429.1|HO044429
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|9900133|gb|BE609101.1|BE609101
EST:     AATTGAAGAAAGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|298168671|gb|HO009601.1|HO009601
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|298198941|gb|HO042304.1|HO042304
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|298185354|gb|HO030567.1|HO030567
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|192324020|gb|FK019311.1|FK019311
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATG
EST: gi|193537152|gb|FK497995.1|FK497995
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAA
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAA
EST: gi|298176820|gb|HO023293.1|HO023293
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|298188341|gb|HO035034.1|HO035034
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|6341881|gb|AW164705.1|AW164705
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|298184082|gb|HO029295.1|HO029295
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|298192412|gb|HO036494.1|HO036494
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
EST: gi|298182314|gb|HO026489.1|HO026489
EST:     AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAACCATAAATGAG                         ATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG
genomic: AATTGAAGAAGGTTAAGAAAAGCAATGGGCAAGTGCTAGCCATAAATGAGgtgtgcactt ... ctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcagtcttattggacaatgaacatggaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA
                                           tgctgat  putative branch site (score: 3)
                               tttgatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatggaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - -aaagaaa
- - - - - - - - agaacaaa
- - - - - - - - - - - - - - tgtattc
- - - - - - - - - - - - - - - - - - - - - - - tgcagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggagg