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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataactttgttggatagagttactactctcctttttttaaaaaaaaaaaaactcgaatcacttattttctattgttttatttgtatag

Basic information

species Glycine max
transcript GLYMA20G32430.1
intron # 48
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 48
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 46
GTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataactttgttgga-tagagttacta-ctctcctttttttaaaaaaaaaaaaactcgaatcacttattttctattgttttatttgtatag
||| | || || || || ||||| ||||||||||||||||| ||||||||||| ||| | ||  |||||||  | || ||||| || ||| |||||||||   |     | |  ||||    | |   || || |    ||| |              | ||  ||  ||  | || |||  |    || |   
GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAGgttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagatacaagtagatgct-ttgcatgtcctgcag--

upper sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 48
lower sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 29
GTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataactttgttggatagagttactactctcctttttttaaaaaaaaaaaaactcgaatcacttattttctattgttttatttgtatag
||||||||||| || || ||||| |||||||||||||| || ||||| ||||||||| | ||  | |||||  |||||||||| |||||  ||||||||| |   |  ||| | | | |    | || | | || |   |||      ||| | |     |||   |||  ||| | |              
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAGgtctgcctcccttggatagctctt-taacaattttcttggattttggtttaaatagat----atcctgtataatctgtag--------------

upper sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 48
lower sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 47
GTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataactttgttggatagagttactactctcctttttttaaaaaaaaaaaaactcgaatcacttattttctattgttttatttgtatag
||||||||||| || || ||||| |||||||||||||| || ||||| ||||||||| | ||  | |||||  | || ||||| |||||  ||||||||| |   |  | ||| | | |    | |    | | ||| ||||    ||     | |  | ||||  | | |||| | |              
GTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgtctgcctc-ccttgatagctct--tcaacttttttcttgtttttttgaacgtccatcatgtatcatctgtattctgtag--------------

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|6566294|gb|AW233969.1|AW233969
EST:     AGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG                         GGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA
genomic: AGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataa ... atttgtatagGGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA
EST: gi|13252146|gb|BG363049.1|BG363049
EST:     AGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG                         GGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA
genomic: AGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataa ... atttgtatagGGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA
EST: gi|6566454|gb|AW234099.1|AW234099
EST:     AGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG                         GGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA
genomic: AGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataa ... atttgtatagGGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA
EST: gi|207829014|gb|GD797724.1|GD797724
EST:     GGAGGAAATTAGGAGAAG                         GGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA
genomic: GGAGGAAATTAGGAGAAGgtatatataa ... atttgtatagGGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA
EST: gi|10231247|gb|BE800063.1|BE800063
EST:     AGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG                         GGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA
genomic: AGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataa ... atttgtatagGGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAGgtatatataactttgttggatagagttactactctcctttttttaaaaaaaaaaaaactcgaatcacttattttctattgttttatttgtatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA