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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggatggctattttgttttcatgtgctatccgcagctgtagatgaaaatatgtacaaatttgagttagacacctatgacaaaaatgctctctattatagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTGCACCTCCTGAAGCCCCGGCTACTGGCTATATG

Basic information

species Glycine max
transcript GLYMA03G31820.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G31820.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM5G831712_T02 (Zea mays), 3'ss of exon 16
atggatggctattttgttttcatgtgctatccgcagctgtagatgaaaatatgtacaaatt----tgagttagacacctatgacaaaaatgctctctattatagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTGCACCTCCTGAAGCCCCGGCTACTGGCTATATG
    |    || ||||  |   | |  |       |  | |  | |     || |||  |     | |||||  | | | | ||   ||  |||  | || ||||||| |||||||| || |||||||| |||||||  ||||| || ||||||||||||||||| || || | |||||||||||||
---aaaatatagtttgcatgtgtatagttcatttggtagcatttaaggtcttgaacatttcttcataagttattcccttctcacggtaaaactcgat-ttgtagGTTCAAGGTTGACGAATTTTGTGGGAATTCTTAGTCAAGGGCTAAGAATTGCACCTCCTGAGGCACCTGTTACTGGCTATATG

upper sequence: GLYMA03G31820.1 (Glycine max), 3'ss of exon 17
lower sequence: AT2G31320.1 (Arabidopsis thaliana), 3'ss of exon 15
-------------------------------------atggatggctattttgt-tttcatgtgctatccgcagctgtagatgaaaatatgtacaaatttgagttagacacctatgacaaaaatgctctctattatagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTGCACCTCCTGAAGCCCCGGCTACTGGCTATATG
                                         |  | ||       ||||||    |    |   || || ||     |   |    ||   |          ||  || |||||        ||  ||||||| | || || || ||||| || ||  | ||||||||||| |||||||||||||| ||||| || |||||||| || |||
gtaagccaactgcaaccagccacatttacatgctttgggaaacagatacaagaaatttcattgtttggttgattctatatatttggctggttgatcatcaaaacccttggttta--accaaaataaatctgctttcagGTTCTCGATTAACGAATTTTGTTGGAATATTGAACCAAGGACTGAGAATTGCACCTCCAGAAGCTCCTGCTACTGGTTACATG

upper sequence: GLYMA03G31820.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv07s0005g03040.t01 (Vitis vinifera), 3'ss of exon 16
atggatggctattttgttttcatgtgctatccgcagctg---tagatgaaaatatgtac--aaatttgagttagacacctatga---caaaaatgctctctattatagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTGCACCTCCTGAAGCCCCGGCTACTGGCTATATG
         | || ||  |||   | || | |  |  |    || | ||||| | | ||  |||||  | | | ||    ||||     || ||  | ||    | ||||||  ||||||||||||||||||| || ||||  |||||||| ||||| || ||||||||||| || || ||||||||||||
--------tttttctgagttctatttcttttcaaaaataaaataaaagaaaaaaggaactgaaattaaaatgaaactaaaatgaagctgaagattttgtcctcaacagGTTCCCGGTTGACAAACTTTGTGGGTATACTTAGTCAAGGACTGAGAATAGCTCCTCCTGAAGCTCCAGCAACTGGCTATATG

upper sequence: GLYMA03G31820.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ30299 (Selaginella moellendorffii), 3'ss of exon 16
atggatggctattttgttttcatgtgctatccgcagctgtagatgaaaatatgtacaaatttgagttagacacctatgacaaaaatgctctctattat----agGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTGCACCTCCTGAAGCCCCGGCTACTGGCTATATG
                                                 || ||      |  | | || ||        |    | || | | | ||    ||||||  |    |||||||| ||||| ||| | | ||||||  |  | || || ||||||||||| ||||||||||||||||||
------------------------------------------------gtacgtttgtcctc-aatgaggcattgtcttgacggctcctgtttgtgatgaaaagGTTCACGCACTACAAACTTCGTGGGAATTTTGAGCCAAGGCTTACGGATAGCCCCTCCTGAAGCACCGGCTACTGGCTATATG

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|208332545|gb|GE129468.1|GE129468
EST:     GTTTGCTCCTTACAGGGATAAACTTGGAAACAGAATGCTCCTATGGCATG                         GTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCA
genomic: GTTTGCTCCTTACAGGGATAAACTTGGAAACAGAATGCTCCTATGGCATGgtaggttgtg ... tctattatagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCA
EST: gi|24136298|gb|BU926808.1|BU926808
EST:     GTTTGCTCCTTACAGGGATAAACTTGGAAACAGAATGCTCCTATGGCATG                         GTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTG
genomic: GTTTGCTCCTTACAGGGATAAACTTGGAAACAGAATGCTCCTATGGCATGgtaggttgtg ... tctattatagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatatgtacaaatttgagttagacacctatgacaaaaatgctctctattatagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTGCACCTCCTGAAGCCCCGGCTACTGGCTATATG
                                          ctctctatt  CT-rich tract
        tacaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggatggctattttgttttcatgtgctatccgcagctgtagatgaaaatatgtacaaatttgagttagacacctatgacaaaaatgctctctattatagGTTCTAGGTTGACAAACTTTGTGGGCATTCTTAACCAAGGACTCAGAATTGCACCTCCTGAAGCCCCGGCTACTGGCTATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-tggatgg
- - - - - - - - - - catgtgc
- - - - - - - - - - - - - - - ccgcagc
- - - - - - - - - - - - - - - - - - - - - - - - -tatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctc