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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaatatttctacttgtcttactttgttgttattttcatccttcctcttgtcataacctgagtgaagaaagaaccttgtatgttattccccacca...

Basic information

species Glycine max
transcript GLYMA01G02480.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G02480.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 11
TTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaatatttctacttgtcttactttgttgttattttcatccttcctcttgtcataacctgagtgaagaaagaaccttgtatgttattccccacca
|||| || |||||||| ||  | ||| |||||||| | ||  |||| ||||||||||| ||| | || |||||||||||||| |||||||| ||||| | |||||   ||   |||        ||   | ||||| |||| |    |   ||||    ||||||  ||   ||      || |  |||  | ||     
TTACCAAACAAGATGAAGGATTTGTTTCTGGTATTCGTGGAGTAGAATGGGATGCTGTAGAGCTGCCCTCTCAGTTCATGGAGAACTGGTGCTACCACAAgtaag---atggatctg-------tatcattttgtttttttaacttgtagccttg----aacctgtttgttaaacagttgtttt--gttggtgccag---

upper sequence: GLYMA01G02480.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G133919_T01 (Zea mays), 5'ss of exon 11
TTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaatatttctacttgtcttactttgttgttattttcatccttcctcttgtcataacctgagtgaagaaagaaccttgtatgttattccccacca
||||||| |||||||| ||  | |||||||| ||| | ||  | || ||||||||||| |||||||| || ||||||||||| |||||||| || || | |||  | | |  | |      | | | || ||| |||  || |  ||  || || |  | |         ||       |||   |||   |  |     
TTACTAAACAAGATGAAGGCTTTGTTGCTGGCATTCGTGGAGTTGAATGGGATGCTGTAGAGTTACCCTCCCAGTTCATGGAGAACTGGTGCTATCACAAgta--tgactggtcc-----atatcagttggtttttagcttgaatctctctttttttttcatt-------agttgatctctttcgtgtctgtatcag---

upper sequence: GLYMA01G02480.1 (Glycine max), 5'ss of exon 11
lower sequence: AT5G10540.1 (Arabidopsis thaliana), 5'ss of exon 11
TTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaatatttctac-ttgtc----ttactttgttgttattttcatccttcc---tcttgtcataacctgagtgaagaaagaaccttgtatgttattccccacca--------------------------------------
|||| ||  | |||||||| || || ||||||||  |    || ||||||||||| ||||| ||||| || ||||| ||||| |||||||| ||||| |||||  |   |    || | ||| |    ||| |||     | |||   |||       | ||||| |      | |        |    ||  |          || |                                      
TTACCAAAGAGGATGAGGGGCTAGTGGCTGGTATCCGGAATATCGAGTGGGATGCAGTTGAATTACCGTCACAGTTTATGGAGAACTGGTGCTACCACAGgtacttgggttcaactgccttgccgaatttaatttacaaatgtttgggtccccgtgatttttgtcctcttacaaatacttttgcagtgctgcgtagaggcatttactagtaaatttataatgaacattatctgaatgtggtttcag

upper sequence: GLYMA01G02480.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 5'ss of exon 11
TTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaatatttcta--cttgtctta---ctttgttgttattttcatccttcctcttgtcataacctgagtgaagaaagaaccttgtatgttattccccacca
|||| ||||| ||||||||||||||| |||||||| | ||||||||||||||||||||||| ||||||||||| ||||||||||| ||||||||||| |||||  |   ||     |  ||| | ||    | |   || | |||||  |  | | |   | | ||| ||  |  |    |  ||  |    | ||    |    
TTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATGCTGTTGAATTACCTTCTCAATTCATGGAAAATTGGTGTTACCACAGgtacttttctaaccaaagtcttatttttaatcctcactgatcttttctgctgttcccagattacaacgtggtt--attttgctccaagagaataatggatct---

upper sequence: GLYMA01G02480.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 5'ss of exon 14
TTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagt----aa--atatttctacttgtcttactttgttgttattttcatccttcctcttgtcataacctgagtgaagaaagaaccttgtatgttattccccacca
|||| ||||| ||||||||||||||| |||||||| | ||||||||||||||||||||||| ||||||||||| ||||||||||| ||||||||||| |||||  |    ||  | | |  || || |  | | |   || | |||||  |  | | |   | | ||| ||  |  |    |  ||  |    | ||    |    
TTACCAAGCAGGATGAGGGTCTGGTTTCTGGTATTCGGGGGATAGAGTGGGATGCTGTTGAATTACCTTCTCAATTCATGGAAAATTGGTGTTACCACAGgtacttttctaaccaaagtcttatttataat-cctcactgatcttttctgctgttcccagattacaacgtggtt--attttgctccaagagaataatggatct---

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|58024369|gb|CX711110.1|CX711110
EST:     GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAG                         AGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
genomic: GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaat ... gttaccatagAGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
EST: gi|254336792|gb|GR842971.1|GR842971
EST:     GATGCTGTTGAGTTA-CTTCTCAGTTCATGGAAAACTGGTGTTACCATAG                         AGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCT-CC
genomic: GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaat ... gttaccatagAGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
EST: gi|58021287|gb|CX708029.1|CX708029
EST:     GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAG                         AGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
genomic: GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaat ... gttaccatagAGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
EST: gi|58018001|gb|CX704743.1|CX704743
EST:     GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAG                         AGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
genomic: GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaat ... gttaccatagAGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
EST: gi|16284148|gb|BI945931.1|BI945931
EST:     GATGCTGTTGAGTTACC-TCTCAGTTCATGGAAAACTGGTGTTACCATAG                         AGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
genomic: GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaat ... gttaccatagAGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
EST: gi|58022383|gb|CX709124.1|CX709124
EST:     GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAG                         AGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
genomic: GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaat ... gttaccatagAGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
EST: gi|17022026|gb|BM093060.1|BM093060
EST:     GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAG                         AGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC
genomic: GATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaat ... gttaccatagAGAAACTTTAATGGGCATTGCAAAGCATTTTGAAACTGGGGAGAGTCTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACTAAGCAAGATGAGGGTCTGGTTGCTGGTATTAGAGGGATAGAGTGGGATGCTGTTGAGTTACCTTCTCAGTTCATGGAAAACTGGTGTTACCATAGgtaagtaaatatttctacttgtcttactttgttgttattttcatccttcctcttgtcataacctgagtgaagaaagaaccttgtatgttattccccacca

- - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccacc