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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgctcttcagcttcgatttcgcattcctttggtttaaccttcttaaacatttgttcttgtttttttctttggttcttatgttgttgttgtcgtgtgtcgtgtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGTAAGCGCAAGAAAGAGGCACGTCAAGTTCACAAGC

Basic information

species Glycine max
transcript GLYMA02G35500.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
gttcgctcttcagcttcga--------tttcgcattcctttggtttaaccttcttaaacatttgttcttg----tttttttctttggtt-cttatgttgttgttgtcgtgtgtcgtgtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGTAAGCGCAAGAAAGAGGCACGTCAAGTTCACAAGC
|| || ||| |  |  ||         |||    ||| |   | ||    |||| | | ||     ||||    ||||  ||| |      || ||| |||  |    |  || |   ||    |||| || || |||||||||||    ||||| |      |||| || || ||||| ||||||||| | ||||||||||| ||||| ||| ||||||||||||
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC

upper sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 1
gttcgc--tcttcagcttcgatttcgcattcctttggtttaaccttcttaaacatttgttcttgtttttttctttggttcttatgttgttgttgtcgtgtgtcgtgtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGTAAGCGCAAGAAAGAGGCACGTCAAGTTCACAAGC
||| |    | |  | ||| |      ||| |  | |   |    | |  ||||   ||   || ||| |  ||   || |   ||||||  | | ||     || |      |||||||||| ||||||||||| |  || || |    | ||||||| || |  || || |||||||| ||||||||||||||||| ||| ||||||||||||
gttagtatccgtttgtttccaaggaaaatttccctagaagatttatttccaacaaa-gtcagtgatttctgattgtattttgtggttgtttgtattgtcctctgttt-----cagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC
















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|192313831|gb|FK007647.1|FK007647
EST:     ATTCTCTTTCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: ATTCTCTTTCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|4307640|gb|AI444076.1|AI444076
EST:     TGAAACCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: TGAAACCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|7478670|gb|AW666357.1|AW666357
EST:     CTGAAACCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: CTGAAACCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|6071298|gb|AW100685.1|AW100685
EST:     GTTCTGAAACCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: GTTCTGAAACCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|23733288|gb|BU764826.1|BU764826
EST:     GTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: GTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|17519530|gb|BM188572.1|BM188572
EST:     CCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: CCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|298194398|gb|HO041046.1|HO041046
EST:     ATTCTCTTTCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: ATTCTCTTTCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|120491259|gb|EH219426.1|EH219426
EST:     TTCTGAAACCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: TTCTGAAACCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|192328211|gb|FK020444.1|FK020444
EST:     TCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: TCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|192313774|gb|FK007646.1|FK007646
EST:     ATTCTCTTTCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: ATTCTCTTTCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|7588724|gb|AW704513.1|AW704513
EST:     GTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: GTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|151402809|gb|EV272622.1|EV272622
EST:     ATTCTCTTTCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: ATTCTCTTTCTCTTTCTCTGTTCTGAAACCACTCTCGCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
EST: gi|6668126|gb|AW279577.1|AW279577
EST:     GCGTCGTTACCATG                         CCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC
genomic: GCGTCGTTACCATGgttcgctctt ... gtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttttttctttggttcttatgttgttgttgtcgtgtgtcgtgtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGTAAGCGCAAGAAAGAGGCACGTCAAGTTCACAAGC
     ttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgctcttcagcttcgatttcgcattcctttggtttaaccttcttaaacatttgttcttgtttttttctttggttcttatgttgttgttgtcgtgtgtcgtgtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGTAAGCGCAAGAAAGAGGCACGTCAAGTTCACAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG