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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattttcgcatcctaattcttcttaattgactccaatttttgtttccgcgaatgattctgaactttttttattctgttttggattattttttttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGGAAGAAAGGGAAGGAAGTCGACAAGGTTGTGGGCGCAAAGAAGGACGAGC

Basic information

species Glycine max
transcript GLYMA18G49040.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49040.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0066g02560.t01 (Vitis vinifera), 3'ss of exon 2
----------gtgattttcgcatcctaattcttct--taattgactccaatttttgtttccgcgaatgattctgaactttttttattctg--ttttggattattttttt-tgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGGAAGAAAGGGAAGGAAGTCGACAAGGTTGTGGGCGCAAAGAAGGACGAGC
          |  |  | | ||||   ||   | |  |  ||||     ||  | | |   |   || ||  |||  | |||  ||||||  |||||  | |||| |||     |||||||||||||||||||||||   |||||||| |||||||| || ||||||| ||| |||||||||||| | || | |||  | || || |||||||| ||||
gtatgtctaagcaaactccacatctctatctgtgtatttcttgatgatgatgat-gatgatgatgattatgatgatgtgtttggattctgaattttgattcatttctttgctataatagGATGTGGCGCAGGAGTTTACTGTGCAGGCCATGCCGACGTTTGTGTTGTTGAAAAAAGGGAAGGAATTGGAAAGGGTGATCGGGGCCAAGAAGGATGAGC
















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|7684955|gb|AW755603.1|AW755603
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
EST: gi|19937420|gb|BQ081284.1|BQ081284
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
EST: gi|5057919|gb|AI736395.1|AI736395
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
EST: gi|17519888|gb|BM188930.1|BM188930
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
EST: gi|192333447|gb|FK023976.1|FK023976
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
EST: gi|7684952|gb|AW755600.1|AW755600
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
EST: gi|4291394|gb|AI437613.1|AI437613
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTNTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
EST: gi|5761106|gb|AI966469.1|AI966469
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
EST: gi|8669107|gb|BE190214.1|BE190214
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
EST: gi|8283327|gb|BE020888.1|BE020888
EST:     ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCT                         GATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG
genomic: ACAAGTTCAACGACGTTGACTTCGTCAAGATCGACGTCGACGAATTACCTgtgattttcg ... ttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgaatgattctgaactttttttattctgttttggattattttttttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGGAAGAAAGGGAAGGAAGTCGACAAGGTTGTGGGCGCAAAGAAGGACGAGC
                                    ttatttttttt  CT-rich tract
             aactttttttattctg  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattttcgcatcctaattcttcttaattgactccaatttttgtttccgcgaatgattctgaactttttttattctgttttggattattttttttgggaatagGATGTGGCGCAGGAGTTTCAGGTGCAGGCGATGCCGACTTTCGTGTTGTGGAAGAAAGGGAAGGAAGTCGACAAGGTTGTGGGCGCAAAGAAGGACGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG