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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaatgtttctttacctcctctgaaataaatcaacatacattttctttttgctaaaaatgcgttgagtattctttgatggaaaccattattccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGATATACATATAGACCGAGCAAAATCAATGCACTTCAACAAGCTGAACGTC

Basic information

species Glycine max
transcript GLYMA13G37090.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 25
lower sequence: AT5G44240.1 (Arabidopsis thaliana), 3'ss of exon 24
ttaaatgtttctttacctcctctgaaataaatcaacatacattttctttttgctaaaaatgcgttgagtattctttgatggaaaccattattccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGATATACATATAGACCGAGCAAAATCAATGCACTTCAACAAGCTGAACGTC
      || |    |  || |||   || | ||  | || || |   | |  | | |||       |  |    || || |    | || |   || |||||||| ||||  || || |||||||| ||| | ||  | ||||||||||| || ||||| ||||| ||||||||||||  ||| || |||||||||||  
--gtgagtataaaaaagtcatctcctatca-tctccctatatataagtctccccagaaaca-----aacaccaattaattgtt-tctttctcttatgcagCTCATAGTTGGAGCAGGCATGGGTCCTATTTTCGCATTGAAGTACTTCCGCTACACATACAGACCCAGCAAAATCAATATACTCCAGCAAGCTGAACGAA
















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|208337448|gb|GE133150.1|GE133150
EST:     ACAACCGTCATATTGGATAGCAATTTTT                         CTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
genomic: ACAACCGTCATATTGGATAGCAATTTTTgtgagtagct ... ttccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
EST: gi|193569794|gb|FK524473.1|FK524473
EST:     CAATTATGTTTCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTT                         CTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
genomic: CAATTATGTTTCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTTgtgagtagct ... ttccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
EST: gi|10254578|gb|BE822344.1|BE822344
EST:     CAATTATGTTTCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTT                         CTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
genomic: CAATTATGTTTCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTTgtgagtagct ... ttccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
EST: gi|192300036|gb|FG991854.1|FG991854
EST:     CAATTATGTTTCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTT                         CTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
genomic: CAATTATGTTTCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTTgtgagtagct ... ttccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
EST: gi|6666069|gb|AW277528.1|AW277528
EST:     CAATTATGTTTCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTT                         CTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
genomic: CAATTATGTTTCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTTgtgagtagct ... ttccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
EST: gi|208332486|gb|GE129465.1|GE129465
EST:     CAATTATGTTGCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTT                         CTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA
genomic: CAATTATGTTTCGGTTGTGTCGACAACCGTCATATTGGATAGCAATTTTTgtgagtagct ... ttccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttgctaaaaatgcgttgagtattctttgatggaaaccattattccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGATATACATATAGACCGAGCAAAATCAATGCACTTCAACAAGCTGAACGTC
                                          ttattcc  CT-rich tract
        taaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaatgtttctttacctcctctgaaataaatcaacatacattttctttttgctaaaaatgcgttgagtattctttgatggaaaccattattccatacagCTCATGGTTGCGGCGGGGATGGGTCCAATTCTAGCCATCAAGTACTTCCGATATACATATAGACCGAGCAAAATCAATGCACTTCAACAAGCTGAACGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - ctcctct
- - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - acataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatgg