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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactcttttcttaccttttttggtctttctttgcacttgcctttttcttttgcccctgtttttagtcttcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCACTGGGATCCTGACTCAAAGATGTTCACG

Basic information

species Glycine max
transcript GLYMA13G44430.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44430.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G32600.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------gtatactcttttcttaccttttttggtc-----tttctttgc--acttgcctttttcttttgccc-ctgtttttagtcttcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCACTGGGATCCTGACTCAAAGATGTTCACG
                                              ||   ||    |  || || |  | | |     | |||| |   | |||  |  |  | |||     ||| |||   | |   |||||||| || ||||| ||| |||| || || || |||||||| ||||| ||||||||||| ||||| |||||||| || 
gtatgtgttttttttttcttttattcgtgacatttacattctacaagtcatctgggattatagctctagtagcccaacatatcttggtcgaattgtttactgatattgatggttgtgttttcgcattggtttcagGTTCCTAGCACAGAGGTTGATAAATCAACCCCAAAGTTTTTCTCTCACTGGGATCCAGACTCCAAGATGTTTACA

upper sequence: GLYMA13G44430.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 5
--------gtatactcttttcttaccttttttggtctttctttgcacttgcctttttcttttgcccctgtttttagtct---tcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCACTGGGATCCTGACTCAAAGATGTTCACG
         | |  || ||| |||  |||||  ||| ||  ||    ||   | ||  || |  || ||| ||  |  |   |||||| ||||| || ||||| || |||||||| |||||||| ||||||||||| ||||||||||| |||||||| |||||||||
gtactttaatctcatcattttttatgttttt--gtcctttatttttgttatttgttatttatatccatgtgttatggttgtgtcaattgcagGTTCCTAGCACAGAAATTGACAAATCCACTCCGAAGTTCTTCTCACACTGGGATCCCGACTCAAAAATGTTCACG
















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|213591623|gb|DB968147.1|DB968147
EST:     ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAG                         GTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCA
genomic: ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAGgtatactctt ... tcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCA
EST: gi|24205772|gb|BU965025.1|BU965025
EST:     ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAG                         GTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGGTCTTCTCGCACTGG
genomic: ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAGgtatactctt ... tcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCACTGG
EST: gi|213611714|gb|DB960642.1|DB960642
EST:     ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAG                         GTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCACTGG
genomic: ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAGgtatactctt ... tcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCACTGG
EST: gi|6069618|gb|AW099277.1|AW099277
EST:     ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAG                         GTGCCGAGCACGGAGATTGACAAGTNCACTCCANAGTTCTTCTCGCACCTG
genomic: ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAGgtatactctt ... tcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCAC-TG
EST: gi|213595326|gb|DB966506.1|DB966506
EST:     ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAG                         GTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCA
genomic: ATCAGTACCTCTTGTTTGCTGCTGAACCATACGAAATCGTTGCTTTCAAGgtatactctt ... tcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctttgcacttgcctttttcttttgcccctgtttttagtcttcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCACTGGGATCCTGACTCAAAGATGTTCACG
            cttgcctttttctttt  CT-rich tract
                  tttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatactcttttcttaccttttttggtctttctttgcacttgcctttttcttttgcccctgtttttagtcttcaatttcagGTGCCGAGCACGGAGATTGACAAGTCCACTCCAAAGTTCTTCTCGCACTGGGATCCTGACTCAAAGATGTTCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG