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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttcttctcccttctcaaactttacattttagttgactgaaccaataataagaaagttcaattttttgttgtaatctgatgcttatatcttttctttcatccttcttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTAGAGCATAAGGACTCAAGATTAGATAAAAGGAAGATAGGTGGAGAGATCA

Basic information

species Glycine max
transcript GLYMA16G03650.1
intron # 6
splice site 3'
intron type U2

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|31459211|gb|CD401239.1|CD401239
EST:     TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGAT                         GATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
genomic: TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGATgtgtgttctt ... ttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
EST: gi|31475026|gb|CD417054.1|CD417054
EST:     TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGAT                         GATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
genomic: TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGATgtgtgttctt ... ttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
EST: gi|298178136|gb|HO027519.1|HO027519
EST:     TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGAT                         GATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
genomic: TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGATgtgtgttctt ... ttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
EST: gi|6747050|gb|AW317506.1|AW317506
EST:     TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGAT                         GATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
genomic: TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGATgtgtgttctt ... ttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
EST: gi|31472400|gb|CD414428.1|CD414428
EST:     TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGAT                         GATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
genomic: TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGATgtgtgttctt ... ttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
EST: gi|254335324|gb|GR846821.1|GR846821
EST:     TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGAT                         GATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
genomic: TAGGACATGTGATCCACATGCTCGAGGCTGAGGACCTCTTATTCCGTGATgtgtgttctt ... ttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
EST: gi|31305530|gb|CD390733.1|CD390733
EST:     CATGCTCGAGGCTGAGGACCTCTTATTCCGTGAT                         GATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA
genomic: CATGCTCGAGGCTGAGGACCTCTTATTCCGTGATgtgtgttctt ... ttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttgttgtaatctgatgcttatatcttttctttcatccttcttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTAGAGCATAAGGACTCAAGATTAGATAAAAGGAAGATAGGTGGAGAGATCA
             atctgat  putative branch site (score: 4)
                     cttatatcttttcttt  CT-rich tract
                      ttatatcttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttcttctcccttctcaaactttacattttagttgactgaaccaataataagaaagttcaattttttgttgtaatctgatgcttatatcttttctttcatccttcttgtctgtagGATCGAAGGAGTGGAGGAGAATCTTCCCGTTCCCATCGCGATTATCAACTAGAGCATAAGGACTCAAGATTAGATAAAAGGAAGATAGGTGGAGAGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA