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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgatggtccatatcatttcaattatatgttttgtgactaaacattttatgatgtggtgtctgttttgattatatgatgatgtgttttatgcattccaaaaaatgtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGAAACTAATGTTAGCTTGAAGGAGTCTGATGCATGGCCAGCTGAG

Basic information

species Glycine max
transcript GLYMA20G36740.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36740.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 2
gttagtgatggtccatatcatttcaattatatgtttt-gtgactaaacattttatgatgtggtgtctgttttgattatatgatgatgtgttttatgcattccaaaaaatgtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGAAACTAATGTTAGCTTGAAGGAGTCTGATGCATGGCCAGCTGAG
    ||   | ||  | |  |||   ||| || ||||      || |  |    | |    | |  ||||||    |||| |        || ||   || |||  |||| |  | |||||| || |||||||| ||||| || || |||||||||||||| ||| | |||||||| |||||| ||||||| |||||||| ||||| ||||||
----gtccggctctctctttttttt-ttacatatttttactgttatatctcagcttagcctgagcttgttttatccatatcaa-------ttcatttgttacaactaatggtcctacagGTTCTTCTATGCCTCAAGTGCATGCATTTACCCTGAATTCAAGCAGCTTGAAACTAACGTTAGCCTGAAGGAATCTGATGCCTGGCCTGCTGAG

upper sequence: GLYMA20G36740.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 2
-------------gttagtgatggtccatatcatttcaattatatgttttg-tgactaaacattttatgatgtggtgtctgttttgattatatgatgatgtgttttatgcattccaa----aaaatgtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGAAACTAATGTTAGCTTGAAGGAGTCTGATGCATGGCCAGCTGAG
               || ||    | ||| |  ||||       ||  |   |  | ||  | | ||     || | | ||  |  | | |   | ||     || ||||||   |     |   || | |  |||||| || |||||||| ||||| || || |||||||| ||||| ||| | || || ||||| ||||||||||| |||||||| ||||| ||||||
gtatatatacaaatatattgccacttcattttctttctggctggtgaataacttcccaagtaatctagctgatgctatttgactgaagttttcaaagaacctattcatgcataatagtatcattttggtctggcagGTTCTTCTATGCCTCGAGTGCATGCATTTACCCTGAGTTCAAGCAGCTTGACACAAATGTGAGCTTGAAGGAATCTGATGCCTGGCCTGCTGAG

upper sequence: GLYMA20G36740.3 (Glycine max), 3'ss of exon 2
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagtgatggtccatatcatttcaattatatgttttgtgactaaacattttatgatgtggtgtctgttttgattatatgatgatgtgttttatgcattccaaaaaatgttt-ttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGAAACTA---ATGTTAGCTTGAAGGAGTCTGATGCATGGCCAGCTGAG
                                  || || |       |||| |   ||  |  | ||||    | | | |  |   |||  |   |||  |     |||||  |  ||||| |||||||| || |||||||||||||| || || || || |||||||| ||||   |||| |||||||||||||| ||||| ||||| || |||
---------------------------------gttagttagattttgttttcttcggttttcgcagtttacggtttcttaaaacaagttaaaaagattggattttttgtttgctttagGTTCTTTTATGCTTCGAGTGCTTGTATCTATCCAGAGTTTAAGCAGTTGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG

upper sequence: GLYMA20G36740.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S237_14V6.1 (Physcomitrella patens), 3'ss of exon 1
gttagtgatggtccatatcatttcaattatatgttttgtgactaaacattttatgatgtggtgtctgttttgattatatgatgatgtgttttatgcattccaaaaaatgtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGAAACTAATGTTAGC---TTGAAGGAGTCTGATGCATGGCCAGCTGAG
              | | || ||   |  | || | ||||      |  ||||||   |  |   | |    | |||    || |    |   ||  ||  |    ||||||   ||||||||| |||||||| || || || || |||||||||||||| ||  | |||||| |||| |||   ||||||||||||||||| ||||| |||  |
--------------agagcaatttgttgttctgatgtgtgtagggtcgatttatgtcttttttgatatcacaagtatggagtggtagcctgagtgggttt-agtggatgttt---cagGTTTTTCTATGCCTCAAGCGCGTGCATTTACCCTGAATTCAAGCAACTCGAAACTGATGTGAGCAGTTTGAAGGAGTCTGATGCGTGGCCCGCTCTG

upper sequence: GLYMA20G36740.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S171_56V6.2 (Physcomitrella patens), 3'ss of exon 1
gttagtgatggtccatatcatttcaattatatgttttgtgactaaacattttatgatgtggtgtctgttttgattatatgatgatgt-gttttatgcattccaaaaaatgtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGAAACTAATGT---TAGCTTGAAGGAGTCTGATGCATGGCCAGCTGAG
                 | | | ||||  | |  |   | ||  | | |     ||| || |  |  ||   ||  | || |  ||| | ||  ||  |          | | || ||||||||| ||||| || || || |||||||| ||||||||||||||| |||| ||| | ||    ||| |||||||||| || || ||||| |||  |
----------------gtgagtacaatcttct--tcctttaccgatcgtagagagat-tgctcccgtttcaaatcttttggttttgtcggttcctgagtggagttggtggatgttgcagGTTTTTCTATGCTTCAAGCGCGTGTATCTATCCTGAATTCAAACAGCTGGAGACTGACGTGAGCAGCCTGAAGGAGTCGGACGCTTGGCCCGCTCTG

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|298193694|gb|HO040342.1|HO040342
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagtgatg ... gtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
EST: gi|19270441|gb|BM886697.1|BM886697
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTCAA-CAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagtgatg ... gtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
EST: gi|19347576|gb|BM892456.1|BM892456
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagtgatg ... gtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
EST: gi|209703622|gb|BW656578.1|BW656578
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagtgatg ... gtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
EST: gi|15287908|gb|BI471799.1|BI471799
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagtgatg ... gtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
EST: gi|192302093|gb|FG995227.1|FG995227
EST:     ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAGCGGCATTAAGAG                         GNNNNNNNATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA
genomic: ATGATTAGCTTCAACATGATTGAGGCTGCCAGGATTAACGGCATTAAGAGgttagtgatg ... gtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttttgattatatgatgatgtgttttatgcattccaaaaaatgtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGAAACTAATGTTAGCTTGAAGGAGTCTGATGCATGGCCAGCTGAG
    ttttgat  putative branch site (score: 4)
                                            tgtttttcc  putative PPT
                                      aaaaaatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgatggtccatatcatttcaattatatgttttgtgactaaacattttatgatgtggtgtctgttttgattatatgatgatgtgttttatgcattccaaaaaatgtttttccagGTTTTTTTATGCCTCTAGTGCTTGTATCTACCCTGAATTCAAACAGTTGGAAACTAATGTTAGCTTGAAGGAGTCTGATGCATGGCCAGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA