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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA

Basic information

species Glycine max
transcript GLYMA01G37480.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 5
attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
 |||||  | ||   |||       ||       |  |   ||  | | ||||    |   |   |  |||  ||  | || |  || ||      ||||||||||||| |||| |||||||||||||| | ||| ||| | ||||| || || || |||||||| || ||||||||||||||||||||||| ||| |  
gttatt--atatataactaacaccctt---cccattttctttcgctgaccaaaaacattaaaaggtatcttgcta--taatgtggtgttt------gcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGATGACAAAGTGTAAGAGG

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 5
attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcat---tttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
                 |   ||  ||   |  ||| |     | |  | ||||||   ||||   | || |   || |    ||| ||   |  |   ||||||||| ||||  || ||||| |||||||| | ||||||| | ||||| || || || |||||||| ||||||||||| |||||||||||||| | ||   
---------------gttatagagcttcactgtgtcctc---tcctgtttaaatggagatcatgcatctgaccatattatatgtttattatatgttggtgcagCAACGTCCTGCCGACAATGATCGCTATGTCAGGAACTGCCGCAATGGGAGGTCGCCGAAGGAGACCAGGTGGTGGTTTCATGATGACAAAGTGTGATTGG

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 6
attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
                 |    | |||   ||  |||    |   | |     ||||| |   ||| |  |   ||  |||| |  ||||      |||||||||||| |  |||||||| |||||||| ||||||||  | ||||| || || || || ||||| ||||||||||||||||||||||  || | ||   
---------------gttacatattttctctacatcacc--ttgttgaattggtgggtcttgcttttgactg-caatacattacc-gatt------gcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
--attatttaag-attctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
     | |||   ||  ||||  |  || ||   |   |   |  |  |||    || |     | | |  ||   ||    || | ||| ||      |||||||||||| |  || |||||||||||||| | ||||||| | || || || || || |||||||| || |||||||||||||| ||||  || |||| | 
gtgacacttagtcatcatactacttgatctattcaaacctcggtgctctcactccatagccag-actctaactagctaga--atgtattgttt------gcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 5
attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
           ||  | |  |   | ||  ||  || ||| || |||      ||||| |   |||        ||  |||   |  |    ||  |||||||||||| |  ||||| || |||||||| | ||||||  | ||||| || ||||| |||||||| | ||||||||||||||| ||||  || | ||   
----------gttaca-tatttcctctacata--tccttgttcaatcg----gtgggtcttgctttctgactgcaatacatacatgtaccgatt--gcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGGTCACCAAAGGAGACCACGTGGTGGTTCCATGACGACACTGTGTGATGGG

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 5
attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaat--aactc-----atttcttgatttctttg--gcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
              ||  | | | | |   ||  |  | |||| || |  |  |  ||| | |     | ||||   ||||     |  |    ||   ||||  ||||||||| || |  || |||||||||||||| | ||||||| | || || || || || |||||||| || |||||||||||||| ||||  || ||||  |
-------------gtagcgtttagtcttactaactactcgatctattaaaacctcagtgccctgactccataatcagactctaactagctaacaatgcatttgttgcagCAACGTCCAGTGGACAATGACCGCTATGTCAGGAACTGCCGCAACGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGACGACACGGTGTAATTGA

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G018447_T02 (Zea mays), 3'ss of exon 5
attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaat--aactc-----atttcttgatttctttg--gcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA----------
              ||  | | | | |   ||  |  | |||| || |  |  |  ||| | |     | ||||   ||||     |  |    ||   ||||  ||||||||| || |  || |||||||||||||| | ||||||| | || || || || || |||||||| || |||||||||||||| ||||  || ||||  |          
-------------gtagcgtttagtcttactaactactcgatctattaaaacctcagtgccctgactccataatcagactctaactagctaacaatgcatttgttgcagcaacgtccagTGGACAATGACCGCTATGTCAGGAACTGCCGCAACGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGACGACACGGTGTAATTGAGCGCCTGTCA

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
-----attatttaagattctac-tggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
        |||| |  |   ||    || |||   ||     ||| |  | |  | |    |         |      ||  || |||  | |||  |  |  |||||||||||    ||||| || || ||||| ||||||||||  || || || || || || ||||||||||||||||||||||| ||||| || |||| | 
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattg-tcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
----------attatttaagattc--tactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
           || ||   | |||  || ||   | || |   |    | || |  || || |  |  |   |        | |||   |  ||| ||      | | ||||||||||||||  ||||| || || ||||| |||||||| |  ||||| || || || |||||||| ||||||||||||||||| ||||| || | ||  |
gttctttcttcttcttcgtgtttccctattgacaagtt-acccaaagtactg-tgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 5
attatttaagattctact--ggtgaatttaggt-aggtcatt--gatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
   |||| | ||||   |    |||||||   | | || |||  |||  | |||        |     || |  |  |  ||| ||    |  || |||   |||    | ||    ||| | || || ||||| | ||| ||| ||||||||||||| |||||||| ||| |||||||||| ||||| || ||||||| |   |
---attttacattcgcgtcaaatgaatttccttcaagtaattttgatttaccatgtgcaatttaagtattcgattggactactgata--ctcgttgcttgaacagGCCAGACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGATCTCCCAAGGAAACACGGTGGTGGTTTCATGACGATAAAGTATGAGTTA

upper sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 5
----attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
       || |   | |  ||  ||| |   ||| |   |  |||| | | |     ||| ||| ||| |  |   | || | ||| | |   |  |    |||    | ||    ||| |||| |  |||||   ||||||| ||||||| ||||| |||||||| ||  ||||||||||||| ||||||||||||| |    
cggtgacatctcgtagtgcacaagtgtaa--agggatacccctgatacctgaagtggtggttgt-attgtatcactacaaat-attgcgtatgtggtgcaacagGCGAGACCACCTGATGATGATCAGTATGTGCGGAACTGCCGAAATGGAAGATCGCCCAAGGAAACTCGGTGGTGGTTCCACGATGACAAAGTATGA----

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|209697785|gb|BW663924.1|BW663924
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAG
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAG
EST: gi|31469425|gb|CD411453.1|CD411453
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
EST: gi|15664810|gb|BI702173.1|BI702173
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
EST: gi|10844680|gb|BF067906.1|BF067906
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
EST: gi|9204241|gb|BE330465.1|BE330465
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
EST: gi|20813348|gb|BQ297826.1|BQ297826
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
EST: gi|37994961|gb|CF806550.1|CF806550
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
EST: gi|20813177|gb|BQ297655.1|BQ297655
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
EST: gi|209697863|gb|BW663925.1|BW663925
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
EST: gi|27445947|gb|CA953070.1|CA953070
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
EST: gi|37996938|gb|CF808527.1|CF808527
EST:     GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG                         CAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA
genomic: GTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGgtgagaattt ... tctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA
                                   tttcttgatttcttt  CT-rich tract
                        ttaataactcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - tctactg
- - - - - - - - - - - - - - - - - - - - - ccatcat
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgggtgt