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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA

Basic information

species Glycine max
transcript GLYMA18G49060.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
ttcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatg---aattgtgcaGA--AGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----
         ||| ||    ||   ||  | |  | |  | |  | ||   |      | | |    |  |  || |||| ||     | ||   ||||||    |  |||||| || ||||| || ||| | |||||||||| ||| |||||||||||||| || || ||||||||||| |||||||||||| |||| || || |    
-------gttgcgttaaatttg--gcccaactgtttcatttcagtataactctattctgaagtgtcttgtatttatctgatatttgtcttggataattgtattaaacagGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA

upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------------------------------ttcctataatgcat-tgttctttctgctta--gcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----
                                                                                      ||    ||   | | ||   | | || | |  |||   | ||  | |||    |  |  |||   |     ||||  |  |  ||  |   |||| |     | | |||||  | ||||| |||||||| |||||||||||  |||| ||||| || ||||| ||||||||||| || |||||||||||  ||||||| || |    
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatctta-tatgatttatgattcacctata-gGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA

upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
ttcctataatgcattgttctt--tctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----
     |  ||    ||| ||   | ||   ||   | || | |||     |   || | | |       |||     |||  |||||    |    | |  |  || ||| |||||||| || ||| | || |||||||||||||| ||||||||||| ||||| || |||||||| |||||||||||| ||||||| ||||    
-----aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacat-cttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA

upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------------ttcctataa---tgcat--tgttctt-tctgcttagcactattctctttgaattttttatgca----taaggaagttcattgttttctggtaa-caaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----
                                                                                     || ||| |    ||||  ||||||  | |  |||    | |    |  | ||  ||||   |     | |||| |      | ||   |||| |||   ||  || | | | ||||||  | ||||| || ||| |||||||||||||  ||||||| || || ||||| ||||| ||||| || |||||||||||  |||| || || |    
gtatgtatctggcttattccttaatgattggagcactaacttctgtttaggattcacctttttttcttaagcaaataatcgtgtatcatatgagggcgcatgatgttctcctgtatttatttgtgtagcttaggcatcctttaaatagtatcatggaaatgttgaatcttaaagtaaacaattctgctttctactgtagGGTCTCTTCCTCTCCCATGGGCTATCAGAATGAAGGTTGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTA

upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G01300.1 (Arabidopsis thaliana), 3'ss of exon 3
---ttcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----
    |   | ||  ||  || |||| ||  |       || ||||   | || | ||  ||  | || |   ||  ||| ||     |    ||  | |||  |||||||| ||||||||||| ||||| ||  | ||||| |||||| | ||||||||||| |||||   ||| || || |||||||||  ||  || || |    
tgtgtttaaaaagacacagtgcttt-tgtatgat----ttatcttctcagttatcattgat--gcaaatctttttatttgtgaattaacttgtgcttcgtgttgaagGGTCCTTGCCTCTTCCATGGTCAATTCGGATGAAGATTGCATTAGGTGCTGCAAAGGGTCTCAGTTTCCTTCACGAAGAAGCTTTAAAGCCGGTCATTTA

upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
ttcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----
                     | ||  ||   | |  |  ||| || || || | |||    || |   || | || || ||       |    |||  | ||||||| ||||||||||||||||||||| | ||||| |||||| | |||||||||||||||||   ||| |||||||||||||||   |  ||||| |    
--------------------gtatgtataaatcaaaccattttaaagttgtt-tccatgtttaa-tcgtttttcttatgatactggtgctttcatgttta-aagGGTCCTTGCCTCTTCCTTGGTCTATCCGGATGAAGATTGCATTAGGTGCTGCAAAAGGTCTCAGTTTCCTCCATGAAGAAGCTTTGAAGCCTGTTATATA

upper sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 2
ttcctataatgcattgttc-tttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA----
    |||  |  || |      |||||  | |  | |||| | |||    |||  |  |        | |||    | |  |  |     | | ||| |   | ||  | || ||||| ||||||||| |  |||||||||||||||||||||| || |||||||| || ||||| || ||||||||| | |  || || |    
---gtatg-tctatcgcaaacctctgcacatc-ttcttctttctgagggctttgag-gtgtctcgtctaattaccatgttttt-cttttttcatttgggttcagGGACC-TTACCTCTCCCTTGGTCTGTTCGAATGAAAATTGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATA

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|17400429|gb|BM177211.1|BM177211
EST:     TGGTTTATGAATGTATGCCCCGTGGAAGTTTGGAGAACCACCTCTTCAGA                         AAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGT
genomic: TGGTTTATGAATGTATGCCCCGTGGAAGTTTGGAGAACCACCTCTTCAGAagtatgcttt ... gaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGT
EST: gi|9820922|gb|BE556432.1|BE556432
EST:     TGGTTTATGAATGTATGCCCCGTGGAAGTTTGGAGAACCACCTCTTCAGA                         AAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGT
genomic: TGGTTTATGAATGTATGCCCCGTGGAAGTTTGGAGAACCACCTCTTCAGAagtatgcttt ... gaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA
                                tggtaac  putative branch site (score: 2)
                       attgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcctataatgcattgttctttctgcttagcactattctctttgaattttttatgcataaggaagttcattgttttctggtaacaaccatgaattgtgcaGAAGGGTCGTTGCCTCTTCCTTGGTCTATCAGAATGAAAATTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - -aatgcat
- - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaccat