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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttttgtgcattgagttgcctggtaaaaattaaatatggaattcaccaattgatatgagtgctaatgctataaatttatactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTACTTAGCTTTCTCATCTGAAGAGATACCAAATGGAGATACTCGTTTTAAGT

Basic information

species Glycine max
transcript GLYMA15G07910.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07910.3 (Glycine max), 3'ss of exon 10
lower sequence: AT4G04955.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgttttgtgcattgagttgcctggtaaaaattaaatatggaattcaccaattgatatgagtgctaatgctataaatttatactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTACTTAGCTTTCTCATCTGAAGAGATACCAAATGGAGATACTCGTTTTAAGT
|| ||       |  ||  |  | | |  | |  ||| |||   |  |  ||| | ||   |  |    || |  ||  |    ||  ||||||||||| |    || |||||  | | |||||| || ||||| |||||| ||||||||||| | |||||||| ||| | || ||||||||||| || |
gtattcaagagttcaagcag--tagaagcactagaatttggttgtatctcatt-acatattttttttgtctttggatgga----gtaaagGAAGCAAAAGGCAAAGGAGACAGTGTTACTGTTGAAACATGTCCACATTACCTAGCTTTCTCAGCCGAAGAGATTCCAGAAGGTGATACTCGTTTCAAAT
















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|193546696|gb|FK503657.1|FK503657
EST:     TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
genomic: TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
EST: gi|193355031|gb|FK321254.1|FK321254
EST:     TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
genomic: TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
EST: gi|6566735|gb|AW234367.1|AW234367
EST:     TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
genomic: TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
EST: gi|193684466|gb|FK623562.1|FK623562
EST:     TTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
genomic: TTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
EST: gi|193387047|gb|FK352464.1|FK352464
EST:     TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
genomic: TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
EST: gi|208192247|gb|GD990193.1|GD990193
EST:     TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
genomic: TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
EST: gi|208024351|gb|GD825983.1|GD825983
EST:     TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGAC
genomic: TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGAC
EST: gi|193472532|gb|FK434917.1|FK434917
EST:     TTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
genomic: TTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
EST: gi|208055588|gb|GD854079.1|GD854079
EST:     TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
genomic: TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
EST: gi|208300854|gb|GE097749.1|GE097749
EST:     TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAG                         GAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC
genomic: TTCACATTGTTCACTTGTCTGATTCAAGTGCTTCCTTGGATCTGATTAAGgtgttttgtg ... tactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatggaattcaccaattgatatgagtgctaatgctataaatttatactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTACTTAGCTTTCTCATCTGAAGAGATACCAAATGGAGATACTCGTTTTAAGT
                          tgctaat  putative branch site (score: 2)
                             taatgctataaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttttgtgcattgagttgcctggtaaaaattaaatatggaattcaccaattgatatgagtgctaatgctataaatttatactgttcagGAAGCAAAAAGTCGTGGTGACAGCATAAGTGTTGAGACTTGTCCCCATTACTTAGCTTTCTCATCTGAAGAGATACCAAATGGAGATACTCGTTTTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT