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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatatgtggactaattaaactataactttatggaaacattttcatgatatacatctgctgattcttcaatatccttgtttcttttcgaaattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG

Basic information

species Glycine max
transcript GLYMA01G03940.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03940.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G60060.1 (Arabidopsis thaliana), 3'ss of exon 1
-catatatgtggactaattaaacta--taactttatggaaacattttcatgatatacatctgctgattcttcaatatccttgtttcttttcgaaattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
   |   | ||   |    ||| ||  ||| |||     || |    ||     | ||  || | | | |  | |    |  |||| | | |     |   || ||||| || ||||| |||||||||||||||||||| ||||| || || ||
ttgtgagtttgttttggggaaaataggtaatttttcattaagaaacacaaatctttcaa-tggtaaatatgtactg--atcatttcatgttgttggcaagcagATGGGATGGTCAAGGAGCTTATGATAGATCAAGAGGGAACAGGAGAAACTG
















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|298190071|gb|HO032192.1|HO032192
EST:     GTTTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAA                         GTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
genomic: GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAAgtaaggagaa ... aattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
EST: gi|193609384|gb|FK562976.1|FK562976
EST:     GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAA                         GTGGGAAGGACAAGGGGCTTATGATAGATCAAG
genomic: GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAAgtaaggagaa ... aattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAG
EST: gi|12689978|gb|BG156314.1|BG156314
EST:     GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAA                         GTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
genomic: GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAAgtaaggagaa ... aattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
EST: gi|298168957|gb|HO020261.1|HO020261
EST:     GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAA                         GTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
genomic: GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAAgtaaggagaa ... aattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
EST: gi|298188019|gb|HO031976.1|HO031976
EST:     GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAA                         GTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
genomic: GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAAgtaaggagaa ... aattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
EST: gi|16348841|gb|BI974436.1|BI974436
EST:     GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAA                         GTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
genomic: GTCTACGCAGTCTTCTGGAGGATCTTGCCTAGAAACTACCCTCCACCCAAgtaaggagaa ... aattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatatacatctgctgattcttcaatatccttgtttcttttcgaaattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG
            tgctgat  putative branch site (score: 3)
                                      ttttcgaaattatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatatgtggactaattaaactataactttatggaaacattttcatgatatacatctgctgattcttcaatatccttgtttcttttcgaaattatatagGTGGGAAGGACAAGGGGCTTATGATAGATCAAGAGGAAACAGAAGGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - tgtggac
- - - - - - - - - - - - - - - - - - - - - ttcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -catctgc