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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgcattgatctattcttttttatcaaaatgttgtgcacctgctttcataattcccgtctactctttcagtttttacaagttaatgtcctccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTG

Basic information

species Glycine max
transcript GLYMA11G08350.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G051129_T01 (Zea mays), 3'ss of exon 3
gttgcattgatctattcttttttatcaaaatgttgtgcacctgctttcataattcccgtctactctttcagtt--tttacaagttaatgtcctccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTG
      ||||   |||      ||  |   ||   |  |     | |  |||||    | |  |||| | |||    |  |  || |  |      ||  ||||| || | ||   ||||||||||||| ||| |||| ||||||||||| ||||| || ||| |   |||||||||||||||||| ||  | |||||| | 
--cttgttgagaaattgcagaatagtattctggcatatattgaatgtagtaattaaattttcatcttgctgttaacgttgagcttgaaatgtatatctatagAGAACCAAATGCTTTGGCATATGCTATCAAGAGATCATGTGAAAACAAAGCTGAAGTGGTGGCACAAGATGAGAAGGAAAGTGGCCTTCGAGCAACACTA

upper sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G573867_T01 (Zea mays), 3'ss of exon 4
----gttgcattgatctattcttttttatcaaaatgttgtgcacctgctttcataattcccgtctactctttcagtttttacaagttaatgtcctccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTG
    ||||     ||  |   |  |||      ||    || |  |  |  | |||||    |||   || | | | || |      |||||  |    || ||||| || | ||   |||| |||||||| ||| |||||||||||||||| |||||||| ||  |   |||||||||||||||||| ||  | |||||| | 
gcttgttgagaaaatgcagaatagttttctggcataaattgaatgtagtaac-taatttttatct-tgctgttaatgttgagcttgaaatgtatttt--tgtagAGAACCAAATGCTTTGGCCTATGCTATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTA

upper sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 4
gttgcattgatctattcttttttatcaaaatgtt--gtgcacctgctttcataattcccgtctactctttcagtttttacaagttaatgtcctccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTG
             ||| |   |||  |   ||       ||    | || | |      ||||| ||  | |      |     | ||    | ||  |||| |||||   || | | || | ||||||||||||||| |||||||||||||| || ||||| ||   ||||||||| ||||| ||  || | ||||| || 
----------gtaattttacgttacaagtgtgcccaaaacaaaaacattgagatcatgagtcta-tccctgaaaaaacattgtgtgataatattcatcgcagGGATCCAGCTGCATTAGCTTTTGCTATAAAGCGATCATGTGAAAACAAGGCAGACGTTGTATCACAAGATGAGAAAGAAAGCGGCTTGCGAGCAACCTTA

upper sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 4
---gttgcattgatctattcttt-tttatcaaaatgttgtgcacctgctttcataattcccgtctactctttcagtttttacaa-gttaatgtcctccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTG
   |||   |  ||     |  |  ||     |   ||||     |  ||  |||  | | |       | |||    | | ||   |  | |  |||  ||||| |||||  ||| | |||| |||||||| |||||||| |||||||||||||||||||| || || ||||||||||||||||||||||||||||| ||||||
caagttatctgcattggggccatgcttggtccatccttgt-----tatttgtatagcttctgagaggaatgtcatgcatgaaaataatggtttggtcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGCTGAGGTAGTATCTTTAGATGAGAAGGAAAGTGGACTGAGGGCGACATTG

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|57573973|gb|CX546948.1|CX546948
EST:     GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAG                         AGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
genomic: GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAGgtaaattttt ... tccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
EST: gi|151408017|gb|EV277832.1|EV277832
EST:     GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAG                         AGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
genomic: GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAGgtaaattttt ... tccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
EST: gi|151401299|gb|EV271113.1|EV271113
EST:     GCAGGGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAG                         AGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
genomic: GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAGgtaaattttt ... tccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
EST: gi|23727257|gb|BU761656.1|BU761656
EST:     GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAG                         AGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
genomic: GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAGgtaaattttt ... tccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
EST: gi|57574227|gb|CX547202.1|CX547202
EST:     GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAG                         AGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC
genomic: GCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAGgtaaattttt ... tccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcataattcccgtctactctttcagtttttacaagttaatgtcctccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTG
                                  agttaat  putative branch site (score: 4)
                                          tcctccact  CT-rich tract
                          tttttacaagttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcattgatctattcttttttatcaaaatgttgtgcacctgctttcataattcccgtctactctttcagtttttacaagttaatgtcctccactgcagAGATCCTAGTGTAATGGCATATGCTATAAAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- tgcattg
- - - - - - - - - - - - - - - - - -tgcacct
- - - - - - - - - - - - - - - - - - - - - gctttca