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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG

Basic information

species Glycine max
transcript GLYMA01G35950.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 10
gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtatt-ttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG
                                  |||    |  ||||          ||||  |||    |  | || |    | ||       | |||| ||    || | | |||  |||| || ||||| |||||||| ||||| ||||| ||||||||||| ||||| ||| | ||||| ||||| || |||| |    ||| | | |   |  | |
--------------------------------gtattctaaagcttcgaggcaatagtttata-atacagccgatcctgttatatcatccatagctgttagaataacgatgacttttt--agGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGATGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGGTAATAGTGTTACATCACAAAATG

upper sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 9
gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggac--ttat-tcatatcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG
                                   |||    ||  |    | ||||   |||| | ||      ||| |||  ||| ||||  || |   ||   || |||     |||| ||||||||||||||||||| ||| | || ||||| ||||||||||| ||| |||| || || ||||||||||||||||||||   | |     | |||| ||
----------------------------------gtttaaacatcactatttgtggatcattatattatgaagcaattccttatgagatattcaatttgggtaac-ttgtatg----tttgtagGGAGAAGAAATTTGTGTTGCTTTGCAAACACATATAAATGATGTCATGTTGCGTCGTTACTCCAAAGCTCGATCTGCTGCCAATAGCTTGGTTAATGGAG

upper sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 11
--------------gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG
              |  ||   ||    |   | ||   | | |   | |||     | |      ||  |  ||||| |   ||   ||      | ||||| | |  ||  |||  | |  |||| | || ||||||||||||||||||| ||||||||||| || ||||||||||| ||| |||| |||||||| ||||| || ||||||||  ||||  || |||||| ||
gttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatag-agttctattccattttatgcagGGAGAAGAAATTTGTGTTGCTCTTCAGACGCATATAAATGATGTTATGTTGCGTCGCTATTCTAAAGCACGGTCTGCTGCTAGTGGCTCTATGAATGGAG

upper sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S364_50V6.1 (Physcomitrella patens), 3'ss of exon 13
gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG
                           | |     |  ||  || | |  ||||| ||||    ||  ||  |||| ||||||| |        |||||  |  ||| || || |  | |||| ||||| ||||| ||||| |||||||||||||| |||||||| ||| |||| || || |||| |     |  |  | |   ||| |   |     | |
-------------------------gttattttcgtacctagatcttg--ctttgtacttgcaaatccctatattattttggagat--------ttatttttggtttgtc-ttgtgagcagGGGGAAGACATTTGCGTAGCACTTCAGACACACATTAATGATGTTATGTTGCGGCGATACTCCAGAAACAAAAATATTCCTAATGGGCAGGTATCAAATG

upper sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 11
gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG
                                                                         |  |||||  | | ||   | |  ||  | | | |   |   | | |||| |||||||| || || ||||| |||||||||||||| ||||| ||||||||  | ||||| | | | || |||| |||    ||  |  |  |     
------------------------------------------------------------------------gtgtctttgtggct-ttccgtgtagttcttctctaaatttctgtcgcagGGCGAAGAAATATGCGTGGCTCTCCAGACACACATAAACGATGTGATGCTGCGGAGATATTCAAGAACGCGTTCTGTTGCTAACGGAGCCATACAAAGCA

upper sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 11
gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG
                                                                          |  ||| | |   ||   | |  ||  | | | |   |   | | |||| |||||||| || || ||||| |||||||||||||| ||||| ||||||||  | ||||| | | | || |||| |||    ||  |  |  |     
-------------------------------------------------------------------------gtgtttttgtggctttccgtgtagttcttctctaaatttctgtcgcagGGCGAAGAAATATGCGTGGCTCTCCAGACACACATAAACGATGTGATGCTGCGGAGATATTCAAGAACGCGTTCTGTTGCTAACGGCGCCATACAAAGCA

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|207686444|gb|GD669244.1|GD669244
EST:     AAATGCGAGTTGCAGGTGTTCTTCACATATTTCAGTTTGAAACAAAGCAG                         GGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGACGTAATGCTG
genomic: AAATGCGAGTTGCAGGTGTTCTTCACATATTTCAGTTTGAAACAAAGCAGgtattagcat ... ttctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG
                                     ttttatcattcttt  CT-rich tract
                agttattttatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaagGGAGAAGAAATTTGTGTAGCTCTTCAGACACACATAAATGATGTAATGCTGCGCCGCTATTCCAAAGCTCGATCTGCTGCGGGTGGTCCTTTGAATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC