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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttgctggcttatattattctttacacacacaaagttggggaattttatgccaaatgtttgctgatcaatgttttgttttttgtttggtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCTATTAAGTTCACCGTTGACACCTCTGCTCTCAGA

Basic information

species Glycine max
transcript GLYMA06G15350.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 15
ttctttgctggcttatattattctttacacacacaaagttggggaattttatgccaaatgtttgctgatca----atgtt-ttgttttttgtt--tggtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCTATTAAGTTCACCGTTGACACCTCTGCTCTCAGA
 | |   ||   ||   |||| ||| |   |  || || ||      || ||   |   |||| || |||     ||||| ||  ||  ||||  ||| ||  |||||| || ||||| |||||||| ||||| || ||||| |||||||||||||| || || || |||||||||||||||  ||||   
gtatcaacttctttcacttatgcttgatg-atgcatagctgtaatggttcataa-agtggtttactaatcttcttatgttgtttcttcctgttcatggacacaaaagGGCCTGAAAACAGGAATGTACTATCTACGGTCACGGGCTGCAGCTGATGCCATCAAATTTACCGTTGACACCTCTATTCTCCAG
















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|193483217|gb|FK451046.1|FK451046
EST:     TTTATGCATGGTCCAAG                         GGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCT
genomic: TTTATGCATGGTCCAAGgtagcaacac ... gtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCT
EST: gi|209726802|gb|BW672503.1|BW672503
EST:     AACCCAACTTTGGAAAACTGACTTCCTTGCATTTTTATGCATGGTCCAAG                         GGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCT
genomic: AACCCAACTTTGGAAAACTGACTTCCTTGCATTTTTATGCATGGTCCAAGgtagcaacac ... gtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCT
EST: gi|193654421|gb|FK600573.1|FK600573
EST:     TTTATGCATGGTCCAAG                         GGTCT-AAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCT
genomic: TTTATGCATGGTCCAAGgtagcaacac ... gtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCT
EST: gi|208221212|gb|GE019538.1|GE019538
EST:     AACCCAACTTTGGAAAACTGACTTCCTTGCATTTTTATGCATGGTCCAAG                         GGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGA
genomic: AACCCAACTTTGGAAAACTGACTTCCTTGCATTTTTATGCATGGTCCAAGgtagcaacac ... gtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGA
EST: gi|208192373|gb|GD993749.1|GD993749
EST:     AACCCAACTTTGGAAAACTGACTTCCTTGCATTTTTATGCATGGTCCAAG                         GGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAG
genomic: AACCCAACTTTGGAAAACTGACTTCCTTGCATTTTTATGCATGGTCCAAGgtagcaacac ... gtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAG
EST: gi|193676101|gb|FK616951.1|FK616951
EST:     TTTATGCATGGTTCCAAG                         GGTCT-AAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGC
genomic: TTTATGCATGG-TCCAAGgtagcaacac ... gtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGC
EST: gi|193651046|gb|FK599375.1|FK599375
EST:     TTTATGCATGGTCCAAG                         GGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCT
genomic: TTTATGCATGGTCCAAGgtagcaacac ... gtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatgccaaatgtttgctgatcaatgttttgttttttgtttggtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCTATTAAGTTCACCGTTGACACCTCTGCTCTCAGA
                 tgctgat  putative branch site (score: 3)
                         aatgttttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttgctggcttatattattctttacacacacaaagttggggaattttatgccaaatgtttgctgatcaatgttttgttttttgtttggtcattaaagGGTCTAAAAACTGGAATGTATTATCTTCGATCACGTGCTGCAGCTGATGCTATTAAGTTCACCGTTGACACCTCTGCTCTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - -tgctggc
- - - - - - - - - - - - - acacaca
- - - - - - - - - - - - - - - - - - -gttgggg
- - - - - - - - - - - - - - - - - - - - - - - - -tatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat