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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataggtctggttaattatgattgctgctgatcttgcatgttatggtaattttagtgaaaatacatttgactgatttgatttttgtcatcttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCT

Basic information

species Glycine max
transcript GLYMA15G13080.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------tataggtctggt-taattatgattgct-gctgatcttgcatgttatggtaattt----tagtgaaaatacatttgactgatttgatttttgtcatcttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCT
             ||     ||| | |  ||||| ||  | | |  || ||  | |  || | ||||    ||   | | |||  ||||||  ||||| |    |  |   |  ||||| | ||  |||| || || ||||| ||  ||||||| || |||||||||||||||||| ||| |||||| ||||| ||||| |||||| |||||||||| |
gtcagtccacacataacaacctgctgtgtttatgtttcttagatattcatgtct-tcttgatcatttgccttaaccatactactcttgactcttttgaatccctt--ttgcgattttagTTGCTGTTGAGCCGGTTGAGGTTGTTTCTGAGTCCTGGATATCCATATGAAGAAATTCTAAGGACCTTCCACAATCAGACCAGCATAGTCATGTGCTCAT

upper sequence: GLYMA15G13080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 3
--tataggtctggttaattatgattgctgctgat-cttgcatgttatggtaattttagtgaaaatacatttgactgatttgatttttgtcatcttgt-atttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCT
  |  | || || | || ||  ||||    |  |  ||||| |   |   ||  | |  |    | ||||   ||||| || ||| |||  | || | | |||||| || || || ||||| || || |||||||| || ||||||||||||||||||||| | | ||| |||||||| || || |||||||| |||||||| |
tttgcatgt-tgatcaaataaaattggaattattgtttgcaaga-gtcaaaaactcatggctggttcatt--gctgatatgctttatgtttttttcttaattagGTGCTCCTAAGCCGTTTGAGATTGTTCTTGAGCCCTGGGTATCCATATGAAGAAATTCTGAGGACATTTCACAATCAAACCAGCATAATTATGTGCTCAT
















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|208297701|gb|GE089374.1|GE089374
EST:     GTCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
genomic: GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
EST: gi|6502372|gb|AW203745.1|AW203745
EST:     GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
genomic: GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
EST: gi|6134631|gb|AW133024.1|AW133024
EST:     GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAC                         GTTCTTCTGAGTCCGTT-AAGGTTATTCTTGAGTCCCGGGTATCCATATGA
genomic: GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTC-GTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGA
EST: gi|10709738|gb|BF009462.1|BF009462
EST:     GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
genomic: GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
EST: gi|15664637|gb|BI702008.1|BI702008
EST:     GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
genomic: GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
EST: gi|7640040|gb|AW734349.1|AW734349
EST:     GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
genomic: GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
EST: gi|208076586|gb|GD873975.1|GD873975
EST:     GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTGAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
genomic: GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
EST: gi|16106061|gb|BI893801.1|BI893801
EST:     GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
genomic: GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
EST: gi|6072595|gb|AW101982.1|AW101982
EST:     GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
genomic: GCCCTGATTATGGAGTACTCAGCTGGGATAACAAGCTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
EST: gi|15813092|gb|BI785367.1|BI785367
EST:     CTTGCTGGTGCTCAG                         GTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA
genomic: CTTGCTGGTGCTCAGgtaattttgt ... ttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaattttagtgaaaatacatttgactgatttgatttttgtcatcttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCT
                                        tcatctt  CT-rich tract
            aaaatacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataggtctggttaattatgattgctgctgatcttgcatgttatggtaattttagtgaaaatacatttgactgatttgatttttgtcatcttgtatttagGTTCTTCTGAGTCGTTTAAGGTTATTCTTGAGTCCCGGGTATCCATATGAAGAAATTTTAAAGACCTTTCACAACCAGACAAGCATAATCATGTGCTCCT

- - - tctggtt
- - - - - - - - - - -ttgctgc
- - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg