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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catacatgataatttctgatcgaataatagtataaaatcgttttaaactaacagcatgaacatagactatttactcaaataaagaatcactttttttcagTCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCTCCTGCTCACGTGCTGAGCCGTGGTATCGGTTGGCAGGGAATTGGAATCT

Basic information

species Glycine max
transcript GLYMA08G12360.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12360.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv10s0003g01460.t01 (Vitis vinifera), 3'ss of exon 8
catacatgataatttctgatcgaataatagtataaaatcgttttaaactaacagcatgaacatagactatttactcaaataaagaatcacttttttt-cagTCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCTCCTGCTCACGTGCTGAGCCGTGGTATCGGTTGGCAGGGAATTGGAATCT
     || ||    | ||  |     | |  | |  ||           || | |||  | || || || |      || |     |   | ||||  |||||||| || || || || ||||| || || || |||||||||||||||||||| || ||||| || ||||| |||||||| ||||||             
---gtattatg-catgtgccctgcacacaacagaggatt---------caagatcatagatattgagtactggtaataacagtttgtatttattttggcagTCAACTGGAGCTTATAAGGCTGCGTCTCGGCTAGCAAGTGCCACACCACCTCCAGCCCACGTCCTTAGCCGGGGTATCGGCTGGCAG-------------
















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|193456119|gb|FK417489.1|FK417489
EST:     CTGGCCATGCTTTTGGAATGATGGCTGCTGTGTTAGTCTCATTAGTTGAG                         TCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCT
genomic: CTGGCCATGCTTTTGGAATGATGGCTGCTGTGTTAGTCTCATTAGTTGAGgtattgacac ... tttttttcagTCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCT
EST: gi|22525738|gb|BU084549.1|BU084549
EST:     CTGGCCATGCTTTTGGAATGATGGCTGCTGTGTTAGTCTCATTAGTTGAG                         TCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCT
genomic: CTGGCCATGCTTTTGGAATGATGGCTGCTGTGTTAGTCTCATTAGTTGAGgtattgacac ... tttttttcagTCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCT
EST: gi|58014211|gb|CX700953.1|CX700953
EST:     ATGATGGCTGCTGTGTTAGTCTCATTAGTTGAG                         TCAACCGGGGCATACAAAGTTGCATCACGTCTTGCAAGTGCCACACCACCT
genomic: ATGATGGCTGCTGTGTTAGTCTCATTAGTTGAGgtattgacac ... tttttttcagTCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCT
EST: gi|58024713|gb|CX711454.1|CX711454
EST:     GCTGCTGTGTTAGTCTCATTAG-TGNAG                         TCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACC
genomic: GCTGCTGTGTTAGTCTCATTAGTTG-AGgtattgacac ... tttttttcagTCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACC
EST: gi|22525586|gb|BU084397.1|BU084397
EST:     CTGGCCATGCTTTTGGAATGATGGCTGCTGTGTTAGTCTCATTAGTTGAG                         TCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCT
genomic: CTGGCCATGCTTTTGGAATGATGGCTGCTGTGTTAGTCTCATTAGTTGAGgtattgacac ... tttttttcagTCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactaacagcatgaacatagactatttactcaaataaagaatcactttttttcagTCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCTCCTGCTCACGTGCTGAGCCGTGGTATCGGTTGGCAGGGAATTGGAATCT
 aactaac  putative branch site (score: 1)
                                         tcactttttttc  putative PPT
                               aaataaagaatcactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catacatgataatttctgatcgaataatagtataaaatcgttttaaactaacagcatgaacatagactatttactcaaataaagaatcactttttttcagTCAACCGGGGCATACAAAGCTGCATCACGTCTTGCAAGTGCCACACCACCTCCTGCTCACGTGCTGAGCCGTGGTATCGGTTGGCAGGGAATTGGAATCT

catacat
- - - - - - - - - - - - - - - - - - - - - - - actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa