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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCGTCTCGCTTCTCCATTCCTTCATTCCCACTCACTGGCTTCCTTTCTCCATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttaccttcttctctctctctctaattgctatgtttcttgcgtttagggattgtgcttttctctcttctgtttcgatgtgagtcagcagacagaaa...

Basic information

species Glycine max
transcript GLYMA02G44180.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G44180.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv06s0009g01580.t01 (Vitis vinifera), 5'ss of exon 1
ACCGTCTCGCTTCTCCATTCCTTCATTCCCACTCACTGGCTTCCTTTCTCCATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacct----tcttctctctctct----ctaattgctatgtttcttgcgtttagggattgtgcttttctctcttctgt-ttcgatgtgagtcagcagacagaaa
||||| ||||||||||| |||||||| ||||| || ||||| ||||| ||||| || || ||||| |||||||||||||||||||  || ||  ||||||||  |||  |     | ||| |  | |||    ||||| |  || ||||||   ||| |  |      |     |  |||||  ||| || ||       | |      
ACCGTTTCGCTTCTCCACTCCTTCATCCCCACCCATTGGCTCCCTTTTTCCATCGTTGGCCGCGCCCAGAAATGGACTCTCTCCAAGACACTTTTCGTCAgtgagttgaccaaaattttcccattttcttagcctaatggtcatttttctt---tttggcaaaaaaaataaggccatttctgcattcaatctgttcagataaa------
















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|23064561|gb|BU579334.1|BU579334
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacc ... tttcatgcagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|151411756|gb|EV281567.1|EV281567
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacc ... tttcatgcagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|7042409|gb|AW472303.1|AW472303
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacc ... tttcatgcagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|8826794|gb|BE210524.1|BE210524
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTATGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacc ... tttcatgcagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|6566899|gb|AW234531.1|AW234531
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacc ... tttcatgcagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|298166995|gb|HO010434.1|HO010434
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCCCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacc ... tttcatgcagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|192331413|gb|FK022718.1|FK022718
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacc ... tttcatgcagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCGTCTCGCTTCTCCATTCCTTCATTCCCACTCACTGGCTTCCTTTCTCCATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttaccttcttctctctctctctaattgctatgtttcttgcgtttagggattgtgcttttctctcttctgtttcgatgtgagtcagcagacagaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcttc