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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccttttttttttctacctacacacttcgaagatgattcctaacctttttagcttcttgtacactgctgatatctatgcacctaatttacaattttcagGCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGCGAGAGTC

Basic information

species Glycine max
transcript GLYMA15G13910.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 12
--------------------------------------------------------------------------------tcccttttttttttctacctacacacttcgaagatgattcctaacctttttagcttcttgtacactgctgatatctatgcacctaatt-tacaattttcagGCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGCGAGAGTC
                                                                                |     |  ||  | ||  || |   |      ||||| | ||| ||   ||  |  | ||  |  |  |   |  |   | ||| || ||   |||  |||| || ||||| |||||||||||||||||||| ||  ||| |||||||||||| ||||||  ||| ||  |||  ||| | |||||||||||| |    |
gtactacattctatctgttgcccaagtcttatctgcattgctaaatgctgttcacgtttgctatttaaaaaactgaattttgagaatccttcatttatgtagaggttgtttttatgatgc-taaactccctacatgttcgttaagcgtggcattacagttagctagttatatcttttgtagGCAGAACATGGCCCAGATAGTCAGGTTGTTCTAGTTGTTGCTGGAGATGGTGTTGATCTGGGTGCCATTGAGGCAGAAGTTAGCAAGCAGTGCAACGCGC

upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------tcccttttttttttctaccta-cacacttcgaaga-----tgatt-cctaacctttttagctt---cttgtacactgctgatatct-atgcacctaatttacaattttc-----agGCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGCGAGAGTC
                 ||    ||||| || || || |    || ||     ||  | ||| |  | ||||  |    | |  | |  || | || ||  | ||  |  |||     ||||     |||| |||||||||||||||||||| |||||||||||  |||| || ||| |||| ||||| || || ||  | || ||| |   |||||||||| | || |
gtatttccatgaaaaagttgcaattttcaacataacatatcgggatgagtttgtgtctgccttatttgtttaattcagacctacagagagcggctaacttgtacatttctttttttggtttctctgcagGCGGAGCATGGTCCAGATAGTCAAGTTGTTCTTGTAGTTGTGGGCGATAGTGTAGATCTCAACGCCATCGAAGAAGAAATTGCCAAGCAGTGCAAAAGCC

upper sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 12
tcccttttttttttctacctacacacttcgaagatgattcctaacctttttagcttc---ttgtacactgctg-atatctatgcacctaatttaca-attttcagGCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGCGAGAGTC
         | |||| |  | ||    |  |  |   ||  |||  | | |   |||   ||  | |||  |  ||  ||        |||| ||  |||| |||||||||||||| || |||||||||||||||||||| |||| ||| ||||| ||||| || |  || ||  |||||||| |||||||||||||| | || |
-----cccctatttccatatgcatgtgtaaagcaaagtttttaagttctctgctttcaattttcatactatttcatccctgatgtttcaattgacttatttccagGCTGAGCATGGCCCTGATAGTCAGGTTGTTCTTGTAATTGCTGGGGATGGCGTGGACCTAAGGGCTATTGAGGAGGAAATCAGCAAGCAGTGCCAAAGCC

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|12772188|gb|BG237115.1|BG237115
EST:     CAGACAAGCATGCAATTCCTTCTCATGTAGCAGCTGATTTGCTTTCCCAG                         GCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGT
genomic: CAGACAAGCATGCAATTCCTTCTCATGTAGCAGCTGATTTGCTTTCCCAGgtttaataag ... caattttcagGCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGT
EST: gi|254340468|gb|GR850770.1|GR850770
EST:     AGACAAGCATGCAATTCCCTTCTCATGTAGCAGCTGATTTGCTTTCCCAG                         GCTGAGCATGGTCCAGATAGTCAG-TTGTTCTTGTGATTGTTGGAGATGGT
genomic: AGACAAGCATGCAATTCC-TTCTCATGTAGCAGCTGATTTGCTTTCCCAGgtttaataag ... caattttcagGCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttagcttcttgtacactgctgatatctatgcacctaatttacaattttcagGCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGCGAGAGTC
                                   acctaat  putative branch site (score: 3)
                                                ttttc  putative PPT
                                      taatttacaattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccttttttttttctacctacacacttcgaagatgattcctaacctttttagcttcttgtacactgctgatatctatgcacctaatttacaattttcagGCTGAGCATGGTCCAGATAGTCAGGTTGTTCTTGTGATTGTTGGAGATGGTGTGGATCTGAATGCAATACAGGAGGAACTCAGCAAGCAGTGCGAGAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG