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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccttattcccatatgatgtctagtgcaaagactcagaagactgtgttctcagattctgttcataaagttttttaaccttattcattttatttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAACGGCAATTACCATGGCAAACACCATTGCTGGTGAAGAAACTGTGCATAA

Basic information

species Glycine max
transcript GLYMA14G04600.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04600.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G21070.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------cccttattcccatatgatgtctagtgcaaagactcagaagactgtgttctcagattctgttcataaagttttttaaccttattcattttatttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAACGGCAATTACCATGGCAAACACCATTGCTGGTGAAGAAACTGTGCATAA
           |    |      | |    | | |||       |  ||      || | | |||||||  || | |  |||| ||   | |  ||||||         ||||||| |||||||| |  | || || ||||||||||| || ||||||||||| ||||| || ||||| || ||||| ||||||||||| ||||| || ||
atcatgtttatcatcaacgtttttgttgcatttggtgtctga--tgggatatagatgatgtgagattcttatc-tgattttttctagtgtcacccatttt--------cagCTGCATTTGGAGCAGTCCTACATGTTATATCCACTTCTCTCCTTGGTATAACAGCAATCACAATGGCGAATACCATCGCTGGTGAAGAGACTGTTCACAA

upper sequence: GLYMA14G04600.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0009g01580.t01 (Vitis vinifera), 3'ss of exon 1
-------cccttattcccatatgatgtctagtgcaaagactcagaagactgtgttctcagattctgttcataaagttttttaaccttattcattttatttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAACGGCAATTACCATGGCAAACACCATTGCTGGTGAAGAAACTGTGCATAA
        |   ||  | ||||||      |       | || |   |   |  |    |    |||| | ||  ||||| |    |||| |||||     ||| ||||||| ||||||| |||||||| || ||||||||||| || |||||| | || ||||| |||||||||||||  |||||||| || ||||| || |||||
ttcaactgctcaatctcgatatgaaaatcggccagggaattctgctaagaatagtgcttg---ttgtttacaatctttttaacagctatttatttt----tatgcagCTGCATTTGGAGCCATTTTGCATGTGATATCCACTTCGCTTCTTGGTGTCACAGCAATCACCATGGCAAACAGTATTGCTGGGGAGGAAACAGTCCATAA
















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|151413044|gb|EV282852.1|EV282852
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCATCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|298177276|gb|HO023523.1|HO023523
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|151395627|gb|EV265504.1|EV265504
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|151405668|gb|EV275482.1|EV275482
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|298193663|gb|HO040311.1|HO040311
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|192326157|gb|FK016964.1|FK016964
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|17021827|gb|BM092861.1|BM092861
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|17021369|gb|BM092403.1|BM092403
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|207820190|gb|GD790040.1|GD790040
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|10709179|gb|BF008903.1|BF008903
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|4291073|gb|AI441709.1|AI441709
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
EST: gi|19053159|gb|BM731826.1|BM731826
EST:     CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCA                         CTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA
genomic: CATTGTCGGTCGCGCTCAGAAATGGACTCTCTCCACCACTCTCATCGTCAgtacgttacg ... tttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctcagattctgttcataaagttttttaaccttattcattttatttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAACGGCAATTACCATGGCAAACACCATTGCTGGTGAAGAAACTGTGCATAA
                         ttttaac  putative branch site (score: 2)
                                        ttttatttc  putative PPT
              ttcataaagtttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccttattcccatatgatgtctagtgcaaagactcagaagactgtgttctcagattctgttcataaagttttttaaccttattcattttatttcatgtagCTGCACTTGGAGCAATTTTGCACGTAATATCCACTTCACTGCTTGGTATAACGGCAATTACCATGGCAAACACCATTGCTGGTGAAGAAACTGTGCATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - tgatgtc
- - - - - - - - - - - - tgcaaag
- - - - - - - - - - - - - - - - - - - - - tgtgttc