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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgagaacttatcttgagcacttcatcaatgtaatgtgaatcttagcaactcagcacaacgtagtccttaactttaacaattgataacttttatgcagCGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTACTGACCAATGCCTTATATGCTGCGATGTGGGAGATCCCTGCAATGCCCG

Basic information

species Glycine max
transcript GLYMA06G19200.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G19200.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G48195.1 (Arabidopsis thaliana), 3'ss of exon 3
tgctgagaacttatcttgagcacttcatcaatgtaatgtgaatcttagcaactcagcacaacgtagtccttaactttaacaattgataacttttat---gcagCGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTACTGACCAATGCCTTATATGCTGCGATGTGGGAGATCCCTGCAATGCCCG
    ||   |  ||||  |   |  |     |  ||      ||   ||  ||          |  |    || ||    | ||  | ||  ||     ||||| |||||||  || ||||| |||||    |||||||||||||| || ||||| || || |||||| | || ||||||||||| | |||||| ||||||||
---agattccaaatctcaatagcaactgatttacaagtcatttccacgctgctacttgtttgatgttaaacaatttatttatttccttacccttgaatggcagCACTTCCTGCAATCGTGGAGACCGTTAGGAGGAAAATCCTGGAGCATATTACAGAACAGTGCCTTGTTTGTTGCGATGTGGGGGTTCCCTGTAATGCCCG
















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|192318587|gb|FK008289.1|FK008289
EST:     CTTTTTTGCTCTTAGAGACTTGATTGATCTTTCCAGAGGAGTCTTTGCTG                         CGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTA
genomic: CTTTTTTGCTCTTAGAGACTTGATTGATCTTTCCAGAGGAGTCTTTGCTGgttagcttct ... ttttatgcagCGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTA
EST: gi|192318586|gb|FK008288.1|FK008288
EST:     CTTTTTTGCTCTTAGAGACTTGATTGATCTTTCCAGAGGAGTCTTTGCTG                         CGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTA
genomic: CTTTTTTGCTCTTAGAGACTTGATTGATCTTTCCAGAGGAGTCTTTGCTGgttagcttct ... ttttatgcagCGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTA
EST: gi|19270920|gb|BM887176.1|BM887176
EST:     CTTTTTTGCTCTTAGAGACTTGATTGATCTTTCCAGAGGAGTCTTTGCTG                         CGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTA
genomic: CTTTTTTGCTCTTAGAGACTTGATTGATCTTTCCAGAGGAGTCTTTGCTGgttagcttct ... ttttatgcagCGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTA
EST: gi|19053024|gb|BM731691.1|BM731691
EST:     CTTTTTTGCTCTTAGAGACTTGATTGATCTTTCCAGAGGAGTCTTTGCTG                         CGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTA
genomic: CTTTTTTGCTCTTAGAGACTTGATTGATCTTTCCAGAGGAGTCTTTGCTGgttagcttct ... ttttatgcagCGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcaactcagcacaacgtagtccttaactttaacaattgataacttttatgcagCGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTACTGACCAATGCCTTATATGCTGCGATGTGGGAGATCCCTGCAATGCCCG
                                      tgataac  putative branch site (score: 2)
                                            cttttat  CT-rich tract
                        ttaactttaacaattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgagaacttatcttgagcacttcatcaatgtaatgtgaatcttagcaactcagcacaacgtagtccttaactttaacaattgataacttttatgcagCGCTTCCTGTGATGGTGGACACCGTGTCCAGGAAAATCCTGGAACACATTACTGACCAATGCCTTATATGCTGCGATGTGGGAGATCCCTGCAATGCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
tgctgag
- - - - - - - - - - cacttca
- - - - - - - - - - - - - - caatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - -cagcaca