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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttgtttgttttgatatacttcttacagggattttgtttaaatttgctatttccatgatatgttgtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG

Basic information

species Glycine max
transcript GLYMA16G26210.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 11
attttgtttgttttgatatacttcttacagggattttgtttaaatttgctatttccatgatatgttgtgttaatttgctatgatcttctttcttt-cttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAG--CAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG
    ||  || |||  | |  |  ||   ||     |||| | || ||   |||  | |  ||      | |  ||| | | || ||  |  |   || ||||||| |||||||| ||||||||||| ||||| || ||||||||||| || ||  |||||       |     |    |  || |||       ||||    
---gtgagtgctttcgtttgttaattttcgg----ctgttcacatatg---tttaaacgg-attccaattcacattgttctcatgtttgtaatccactcagGTTATCAGCAGAGTTGGTGATCTTGTGGGCATCAAGTACTTCCCTGCGGAGCCGCCAAAGATTGCTGAAGCTGATCACGATAAGCTGGAGTAAATGATGA--

upper sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 11
----attttgtttgttttgatatacttcttacagggattttgtttaaatttgctatttccatgatatgttgtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG
     |  ||| | || |  | |  ||   | |   | ||  ||| | | ||    |  ||| |     ||  |   ||| || |   |      |  |   ||||||| |||||||| ||||||||||| ||||| |||||||||||||| |||||| |||||       |||  ||   | | |   || |||  ||  || 
gtgagtgctgtatcttgtttttt-tttggcataaatacttcatttcattctg--ggtgacataacgaactg-atgtgtttcctgtctgcgcaacccacttccagGTTATCAGCAGAGTTGGTGATCTTGTGGGCATCAAATACTTCCCTGCAGAACCACCAAAGATTGCTGAAGCTGGTCATGATAAGCTGGAGTAGGAGCGAA

upper sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G067257_T01 (Zea mays), 3'ss of exon 12
attttgtttgttttgatatacttcttacagggattttgtttaaatt-tgctatttccatgatatgttgtgttaatttgctatgatcttct----ttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG
                  |   | ||| |   | ||  |||  ||| |   | |   |    | | || ||| || || |       | |      |  ||| ||||||| |||||||| || || ||||| ||||| |||||||||||||| |||||| |||||         |  || | | |   ||  ||| | || |   
-----------------gtgagtgttataaatacttcatttttattctaggagtcataaataaagctgagttgatgtgtttcttgtctgtgcaacccactctcagGTTATCAGCAGAGTTGGCGACCTTGTGGGCATCAAATACTTCCCTGCAGAACCACCAAAGATT------GCTGGAGCTGATCATGATAAGCTGGAGTAG-

upper sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 11
attttgtttgttttgatatacttcttacagggattttgtttaaatttgctatttccatgatatgttgtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG
    ||  |||| | | ||||||| |       | || |   | |     ||      ||  || ||||||  ||  || ||         |  ||| ||||||| |||||||| || || ||||| ||||| |||||||||||||| |||||| |||||        ||  |    | | |   || |||  || | | 
---gtgagtgttataa-atacttcatttt----tattctaggagtcataaatagagccgagctgatgtgtttcttgtctgtg----caacccactctcagGTTATCAGCAGAGTTGGCGACCTTGTGGGCATCAAATACTTCCCTGCAGAACCACCAAAGATTGCTGGAGCTGATCATGATAAGCTGGAGTAGGAATCAA

upper sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G357734_T03 (Zea mays), 3'ss of exon 16
attttgtttgttttgatatacttcttacagggattttgtttaaatttgctatttccatgatatgttgtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG
    ||  |||| | | ||||||| |       | || |   | |     ||     |||  || ||||||  ||  || ||         |  ||| ||||||| |||||||| || || ||||| ||||| |||||||||||||| |||||| |||||         |  || | | |   ||  ||| | || |   
---gtgagtgttataa-atacttcatttt----tattctaggagtcataaataaagctgagctgatgtgtttcttgtctgtg----caacccactctcagGTTATCAGCAGAGTTGGCGACCTTGTGGGCATCAAATACTTCCCTGCAGAACCACCAAAGATT------GCTGGAGCTGATCATGATAAGCTGGAGTAG-

upper sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G157249_T01 (Zea mays), 3'ss of exon 4
attttgtttgttttgatatacttcttacagggattttgtttaaatttgctatttccatgatatgttgtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG
    ||  |||| | | ||||||| |       | || |   | |     ||      ||  || ||||||  ||  || ||         |  ||| ||||||| |||||||| ||||| ||||| ||||| |||||||||||||| ||| || |||||        ||  |    | | |   || |||  || | | 
---gtgagtgttataa-atacttcatttt----tattctaggagtcataaataaagccgagctgatgtgtttcttgtctgtg----caacccactctcagGTTATCAGCAGAGTTGGTGACCTTGTGGGCATCAAATACTTCCCTGCAGAAACACCAAAGATTGCTGGAGCTGATCATGATAAGCTGGAGTAGGAATCAA

upper sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 6
attttgtttgttttgatatacttcttacagggattttgtttaaatt-tgctatttccatgatatgttgtgttaatttgctatgatcttct----ttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG
            ||||| |   | ||| |   | ||  |||  ||| |   | |   |    | | || | | || || |       | |      |  ||| ||||||| |||||||| || || ||||| ||||| |||||||||||||  |||||| |||||        ||  |    | | |   || |||  || | | 
-----aaagcccttgatgtcagtgttataaatacttcatttttattctaggagtcataaataaagctgagctgatgtgtttcttgtctgtgcaacccactctcagGTTATCAGCAGAGTTGGCGACCTTGTGGGCATCAAATACTTCCCTGTAGAACCACCAAAGATTGCTGGAGCTGATCATGATAAGCTGGAGTAGGAATCAA

upper sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 11
attttgtttgttttgatatacttcttacagggattttgtt-taaatttgctatttc-catgatatgtt-gtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG---
  ||      || || |   ||| || | |     | ||| | | | |  || |     || |   |   || | |    || | | |   ||  ||| | ||||||| ||| |||| || ||||||||||| |||||||||||||||||  | || |   ||||||||||||| |     |||||    ||  | || |||    
--ttcagaaattgtgttgctcttgtttcggatccatggttatgagtcttttaatgggtgtgctccatccatggttacacact-taaacagtttcttttgtcagGTTATCAGCCGAGTTGGCGATCTTGTTGGTATAAAATACTTCCCTGCGCAGCCCAAGGAGCAGCAACAAGAGGAA---AAAACATCAAAACTGGACTGAAAGT

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|6134994|gb|AW133387.1|AW133387
EST:     TATGCATATCTGCAGCTCATTCAAGGGAGGACCTTATCAAAGCCTTGCAG                         GTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAA
genomic: TATGCATATCTGCAGCTCATTCAAGGGAGGACCTTATCAAAGCCTTGCAGgtatgtatgt ... tctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctatttccatgatatgttgtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG
                      tgttaat  putative branch site (score: 3)
                                ctatgatcttctttct  putative PPT
                      tgttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttgtttgttttgatatacttcttacagggattttgtttaaatttgctatttccatgatatgttgtgttaatttgctatgatcttctttctttcttagGTTATTAGCAGAGTGGGTGATCTTGTTGGCATAAAATACTTCCCTGCTGAACCAACAAAGCAGCAACAAGAAGGGGGTAAAACTGTGAAGTTTGATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - tgctatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctatg