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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatttcattagacaaatttcatcatggatacttagtattattaccctaacggttttcactacctaatgtattaatactgttgtgttgattcatttctagATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGCATTTTTGTGTCCTGCTGATGGATCTATTATGATAACAG

Basic information

species Glycine max
transcript GLYMA20G32030.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 5
-----taatttcattagacaaatttcatcatggatacttagtattattaccctaacggttttcactacctaatgtattaatactgttgtgttgattcatttctagATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGCATTTTTGTGTCCTGCTGATGGATCTATTATGATAACAG
      ||  ||||   |    ||  ||||   ||      ||| |      | | |    || ||    |||   || ||  | || | ||  ||  |||  |||||||||||||||||||| ||||| ||||||||| | ||  |  ||||  |||| ||||| || ||||||||  |||||||||||||||
tgctgcaaggtcatataattgtttgaatcac--atttcccatataacc-tattgaagcacatctcttgaaaattggtttatgtttttttttt--tttttttgcagATTAGCATCAACACCAGCAATGTTTAATAGCACATTGACTGAAGATGAGTCATTCTTGTGCCCAGCTGATGGGGCTATTATGATAACAG

upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 5
taatttcattagacaaatttcatcatggatac--ttagtattattaccctaacggttttcactacctaatgtattaatact---gttg-tgttgattcatttct-agATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGCATTTTTGTGTCCTGCTGATGGATCTATTATGATAACAG
         || || |  ||   ||| |||||  | |  |     |   |    |||||   |  || || | ||| | |     ||| | |   ||| ||| | |||||||| ||||||||||| ||||| ||||||||||| ||  |    |||   |||||||||||||| |||||||| ||||||||||| |
-------tatatactatgttttccatagataccatcatcaagggaaattttgttgttttttttgtctgattttttactgccttgattgatatcatttcttttttcagATTAGCTTCAACACCAGCAATGTTTAATAGCACACTTACTGAAGGCGAACAGTTTTTGTGTCCTGCAGATGGATCCATTATGATAACCG

upper sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S152_87V6.2 (Physcomitrella patens), 3'ss of exon 5
taatttcattagacaaatttcatcatggatacttagtattattaccctaa---cggttttcactacctaatgtattaatactgttgtgttgattcatttcta---gATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGCATTTTTGTGTCCTGCTGATGGATCTATTATGATAACAG
       |  ||   || ||     |  |    || | |    |    ||   | || |  | | |  | || || |||  | ||  ||||     |||| |   |  | |||||||||||||| ||||||||||||||  | |||      || |   |||| ||||||| | | ||  | || ||||| ||||
-----agagcaggtcaaatttgcatttaaccagtactttagacatgtcaaattctgtataaagttcaaattggatcaat-ttcttaggttgtggtgtttccaacagTATGGCATCAACACCAGCGATGTTCAATAGCACCTTAACAGTTCGAGACGACCTTTTTTGTCCTGTTCAAGGGGCGATAATGATTACAG

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|213596832|gb|DB964095.1|DB964095
EST:     AATATNCTCGAGGTCTTACTNGGTGGTGGCCTAGAAGTTGTCCACTACGG                         ATTAGCATCAACACCAGCCATGTTC
genomic: AATAT-CTCGAGGTCTTGCT-GGTGGTGGCCTAGAAGTTGTCCACTACGGgtgggtgata ... tcatttctagATTAGCATCAACACCAGCCATGTTC
EST: gi|208110117|gb|GD904881.1|GD904881
EST:     GCAATATCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGG                         ATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGC
genomic: GCAATATCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGGgtgggtgata ... tcatttctagATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGC
EST: gi|10847956|gb|BF070534.1|BF070534
EST:     GCAATATCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGG                         ATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGC
genomic: GCAATATCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGGgtgggtgata ... tcatttctagATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGC
EST: gi|20448456|gb|BQ252580.1|BQ252580
EST:     GCAATATCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGG                         ATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGC
genomic: GCAATATCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGGgtgggtgata ... tcatttctagATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGC
EST: gi|207736276|gb|GD712547.1|GD712547
EST:     GCAATATCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGG                         ATTAGCATCAACACCAGCCATGTTCAATA
genomic: GCAATATCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGGgtgggtgata ... tcatttctagATTAGCATCAACACCAGCCATGTTCAATA
EST: gi|208290295|gb|GE082723.1|GE082723
EST:     GCAATGTCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGG                         ATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGC
genomic: GCAATATCTCGAGGTCTTGCTGGTGGTGGCCTAGAAGTTGTCCACTACGGgtgggtgata ... tcatttctagATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaacggttttcactacctaatgtattaatactgttgtgttgattcatttctagATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGCATTTTTGTGTCCTGCTGATGGATCTATTATGATAACAG
                                            ttcatttct  CT-rich tract
                   taatgtattaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatttcattagacaaatttcatcatggatacttagtattattaccctaacggttttcactacctaatgtattaatactgttgtgttgattcatttctagATTAGCATCAACACCAGCCATGTTCAATAGCACACTCACAAAGAATGAAGCATTTTTGTGTCCTGCTGATGGATCTATTATGATAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - -catggat
- - - - - - - - - - - - - - - - - - - - - - ccctaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat