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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatggatttcatgtggtctccaaggcttcaggcactgtagcataattcttatattttctttcttgcagccactcataagaactttttttttgccccagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT

Basic information

species Glycine max
transcript GLYMA16G03670.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 3
------------------------------tgcatggatttcatgtggtct-ccaaggc--ttcaggcactgtagcataattcttatattttctttcttgcagccactcataagaactttttttttgccccagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT
                              |  |     |    ||  ||   |||  |  |||| |||||  |   ||| | | |  |||   | | | |   |||         ||||||||||    ||||||||||| |||||  |  |||||||  | || ||||| |||||||||||||| |||||| |||| || | ||| |||||||||||  ||||||| || |
gtctcactctattcttgtttgtttctgtattaaaccatctcttcgttatccatcaattcaattcaagcactaaa---taactgtaagttttctctccattctaacacatcccctt-cttttttttttttgcagTATTTTCTCTATCAGGTACTACGAGGATTGAAGTATGTGCATTCAGCAAATGTCTTGCACAGAGACCTCAGGCCAAGTAATTTGCTGCTGAATGCGAAAT

upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 3
-tgcatggatttcatgtggtctccaaggcttcaggcactgtagcataattcttatattttctttcttgcagccactcataagaactttttttttgccc-cagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT
    |    | |  | ||||    | ||  | |   | ||   || ||   | |||| |||| |  |  |   | |  || |  |    ||||| |   ||||| ||  ||||||| |||||||||||||| |||||||| || ||||||||| | |||||||| ||||| ||||| || |||||| |  | ||||| ||||
acaaagaactatattttggtacggagggagtaatatattgcttcacaacaatgatatattctataatcta--tatttctatgttccccctttttccttgcagTACTTCTTGTATCAGTTGTTACGAGGGCTAAAATATGTGCACTCAGCAAATATATTGCACCGCGATCTGAAGCCGAGCAATTTGTTCCTAAATGCAAATT

upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------------tgcatggatttcatg--tggtctccaaggcttcaggcactgtagc--ataat--tcttatattttctttcttgcagccactcataagaactttttt------tttgccccagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT
                                                                             |    | || | |||  |  |     |  ||| |        |||  ||||   | |  | | || |   ||| ||       ||  || |  |||      | |    |||| |||||||||||| ||||| || |||||||||||||| |||||||| ||||| ||||| |||||| | || ||||| ||||||||  ||||||| ||||
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagctaataaggatttcgtttgttatgctttgaagttgtgtttagtaattagtttcgattatgttttgcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT

upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
tgcatggatttcatgtggtctccaaggcttcaggcactgtagcataattcttatattttctttcttgca-gccactcataagaactttttttttgccccagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT
    |||  ||  |||     | ||     ||  |  |   | || |||  |||  |  |   ||   | | || | | |      || |  |  |  ||||| || ||||||||  |||||||||| || ||||||||||| ||||||||||| ||||| || ||| | ||||| |||||||||||  ||||||| ||||
actgtgggatttttgtaagtgcaaatataacat-cttttctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT

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|23052819|gb|BU577310.1|BU577310
EST:     TGCATCAAATAATTCGTTCCAATCAGCAATTGACTGATGATCATTGTCGG                         TATTTTCTGTATCAATTGTTACGA
genomic: TGCATCAAATAATTCGTTCCAATCAGCAATTGACTGATGATCATTGTCGGgttagaactt ... tttgccccagTATTTTCTGTATCAATTGTTACGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcttatattttctttcttgcagccactcataagaactttttttttgccccagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT
                                      ctttttttttgcccc  CT-rich tract
                               ataagaactttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatggatttcatgtggtctccaaggcttcaggcactgtagcataattcttatattttctttcttgcagccactcataagaactttttttttgccccagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
-gcatgga
- - - - - tcatgtg
- - - - - - - - - -ctccaag
- - - - - - - - - - - - - - - caggcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccactca