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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA

Basic information

species Glycine max
transcript GLYMA05G26240.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 4
-tctaagtaagttgtgg---tatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
 | ||    | || |||    || |    | ||||| | |||||| ||  |   |||   |    |   ||  |  |||  | ||    |   || |  |  ||  || || |||||||||||||| |||||||| ||||||||||||||  | ||||||||   |||||  || ||||||||  | ||  |||   
ttatagagtatttttggagtaatatcctacgttttagtctgctttcagtct---tcagtgatcttaagattcatggtgttcttttcctctgatttctgctc-agGCATCGGGCTTCCATCTGGAAAGTCACTTTTCCAACTTCAAGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG---

upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g52370.1 (Oryza sativa), 3'ss of exon 4
tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattatta---tattatat-tatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
    |||  |   | |     |||   ||||       | |  |   || ||     ||  || | |  |    |||| |||   | |||| | |    ||||| ||| |||||||| |||||||| || ||||| ||||| ||||||||  ||||||||||||  || |  || ||||||||| | |   ||    
----agtgtggaattgctcagttgctcttttcgataattcttggtccaactctgtctatgtatatatcatggcttatttttaacctcttatttctgccctttagGTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAGTGATA---

upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 4
tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattatta---tattatat-tatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
    |||  |   | |     |||   ||||       | |  |   || ||     ||  || | |  |    |||| |||   | |||| | |    ||||| ||| |||||||| |||||||| || ||||| ||||| ||||||||  ||||||||||||  || |  || ||||||||| | |         
----agtgtggaattgctcagttgctcttttcgataattcttggtccaactctgtctatgtatatatcatggcttatttttaacctcttatttctgccctttagGTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAA---------

upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 4
-----tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
     |  |   |  || |||| |   || | ||||    |  |   | | |    |||    |  ||  |   ||  ||||| || | |        ||   |||||||||||||||||||||||| |||||||| ||||| ||||||||  |||| ||||| |  ||||  || ||||||||| | |    ||| |
ctttgttcatccattttatggtgtaactgaccttttccc-taataacatgatgccccattc--tgtatgatggataacgtatttttttttgggggggcatc--agATATTGGACTTCCATCTGGAAAGTCACTTTTCCAACTCCAAGCTGAACGGATCTTGTGCGTTCAGAAGCTGGCTGCTCAATCCA---GTGAAA

upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 4
------tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
      |  |   |  ||||||| |  ||| | ||||  |    | ||| |    ||   | |  |    |    ||   | || |  ||||      |   | |||||| ||||||||||| ||||| |||||||| || || |||||||| |||||| |||| |  || |  || ||||||||| |||   |     
tctttgttcatccattttgtggtgtaattgaccttttcctaatatgtgatgccccattccgtatgatggatggcgtaacttgttttcctatt------tgcctcagATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA---

upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G35020.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------tctaagtaagttgtggtatttttgtcatttt-aatgtgc--tttgagggtaaatca----------tgaaatacatcttttttattgtattattatatta-tattat-attttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
                                                               || || |||||  | |  | ||||  |  | |||| |   ||  |    | || |          ||  |    | | |||| ||   |||  ||| || | |||| || | |||||| ||||| |||||||| ||||||||||||||  |||||||||||||||| || ||||  || || || ||| |||| || |  | |||| 
gtgagtagttctcatttcagttctgtctttgctgaacatcttctatacgttcttgcaaatttccttagcaagttcagattctcttgttttagtgaatgcgacattcaataacagatgacgtttactgttgttacctgtatattttgttaccttaccataataattttatcatctcagATATCGGACTGCCATCTGGGAAATCACTTTTTCAGATTCAAGCTGAGAGGATCTTATGTGTCCAAAGGCTTGCTTCTCAGGCAATGAGTGAGG

upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s1959g00010.t01 (Vitis vinifera), 3'ss of exon 1
-tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
 |  |    |  | || |   ||| |     |  | |   ||    |  |||  |     | ||  || |  || | |   ||     ||||  || | |||||||||||||||||| ||||| ||||| |||||||||||||||||  | ||||||||||  || ||||| ||||||||| ||||||||||| 
attcagtccatgtttgttgaatttatagaggtggtttttattttcagataattgttcctcaaattcttctgtttatttgtgtacgcc-tatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG

upper sequence: GLYMA05G26240.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 4
tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggt--aaatcat-gaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
      | |||    || | ||     | |  | ||| |||     |  | || || |     ||  || ||   | ||||  | ||   ||||  || | |||||||||||||||||| ||||| ||||| |||||||||||||||||  | ||||||||||  || ||||| ||||||||| ||||||||||| 
---nnntcagtccatgtttgttgaatttatagaggtggtttttattttcagataattgttcctcaaattcttctgtttatttgtgtacgctatttcatgtcagATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG

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|151393104|gb|EV262979.1|EV262979
EST:     GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCA                         ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA
genomic: GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCAgtgagtattc ... tatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA
EST: gi|13480594|gb|BG509937.1|BG509937
EST:     GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCA                         ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA
genomic: GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCAgtgagtattc ... tatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA
EST: gi|254340891|gb|GR854619.1|GR854619
EST:     GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCA                         ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA
genomic: GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCAgtgagtattc ... tatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA
EST: gi|254346278|gb|GR859891.1|GR859891
EST:     GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCA                         ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA
genomic: GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCAgtgagtattc ... tatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA
EST: gi|213600098|gb|DB964304.1|DB964304
EST:     GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCA                         ATATTGGACTTC
genomic: GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCAgtgagtattc ... tatattttagATATTGGACTTC
EST: gi|298168261|gb|HO014436.1|HO014436
EST:     GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCA                         ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA
genomic: GGGACTCGACTTGGAAGTTCAGATCCAAAAGGATGTTTCAgtgagtattc ... tatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA
                atcttttttattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaagtaagttgtggtatttttgtcattttaatgtgctttgagggtaaatcatgaaatacatcttttttattgtattattatattatattatattttagATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT