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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcgttttaccaattcttttacttataaccgacacaggagttaagacttttctttgatatgagaatcttgactaatgaactgcaactaatggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTGAGTTCATACTCAGGCGTGATGGTTATCCAAC

Basic information

species Glycine max
transcript GLYMA02G04320.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04320.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 4
ggcgttttaccaattcttttacttataa-ccgacacaggagttaagacttttctttgatatg-agaatcttgactaatgaactgcaactaatggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTGAGTTCATACTCAGGCGTGATGGTTATCCAAC
                 |   ||||| | || |   |  |  |     ||    |||| |   ||||   | | | || |    |   |  || |     ||||||||| ||||| ||  | |||||||||||||| ||||| || |||||||||||||| |   |||||||||| ||||||| 
--------------gtatgaccttatgagcccatctataatatgtagattagtgttgacaaacagaacagttagttat-attgcctttttctgtttcaatagGTGCTTACAGTGATTCAAGAGGCCTTCCAGGAGTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG
















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|120490920|gb|EH219087.1|EH219087
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|20497810|gb|BQ272740.1|BQ272740
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|120531769|gb|EH259902.1|EH259902
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|120530295|gb|EH258429.1|EH258429
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|37996526|gb|CF808115.1|CF808115
EST:     CAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: CAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|213590180|gb|DB963799.1|DB963799
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|193524670|gb|FK480077.1|FK480077
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|213594062|gb|DB961950.1|DB961950
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|13562529|gb|BG550749.1|BG550749
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|120495797|gb|EH223964.1|EH223964
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
EST: gi|192313436|gb|FK005516.1|FK005516
EST:     TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAG                         GTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG
genomic: TGCAATTGCAAGAGCTAAACACTATCTTTCATTGACCTCGGGTGGTTTAGgtattcatat ... ggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttctttgatatgagaatcttgactaatgaactgcaactaatggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTGAGTTCATACTCAGGCGTGATGGTTATCCAAC
                                      aactaat  putative branch site (score: 2)
       tttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcgttttaccaattcttttacttataaccgacacaggagttaagacttttctttgatatgagaatcttgactaatgaactgcaactaatggtgatgcagGTGCTTATAGTGACTCCCGTGGCCTTCCAGGAGTGAGGAAGGAAGTTGCTGAGTTCATACTCAGGCGTGATGGTTATCCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - ccgacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaac