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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaacattttaaaaaatttattggatgcatacttgccatgcatttgatttagccttgctttgttactgccactacttaaaaatttggtaattcagttttcttattttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTGAATGGTGATGCTGCTGCCTTGATGATTCGAGA

Basic information

species Glycine max
transcript GLYMA05G37650.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 4
-------------gtaagcaacatt-ttaaaaaatttattggatgcatacttgccatgcatttgatttagcctt---gctttgttactgccactacttaaaaatttggtaa--ttcagttttcttat--tttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTGAATGGTGATGCTGCTGCCTTGATGATTCGAGA
              |      |||| |||  |     |     | ||| ||  |  ||| ||   | ||   ||   ||||  |   |   |||   | | ||   ||| |  || |   |   | |  | | || |||| |||||||||||||| ||||| || ||||| ||||||||  | || || ||| | || |||||||| ||||| ||||| ||||| |||||||| || ||
gtaagattgatctttgcatttcattattaggatcgacaaccagttcattctctctgtgccttatctgtacagttaaagcttcatgttttgtactctgttataacagggttaacttgaacctgtgtgtgatattttgcagATCTTGTTAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA

upper sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcaacattttaaaaaatttattggatgcatacttgccatgcatttgatttagccttgctttgttactgccactacttaaaaatttggtaattcagttttcttattttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTGAATGGTGATGCTGCTGCCTTGATGATTCGAGA
             |||      |||   |||     ||    || ||   |||| |  |    |  || |||     | ||   || ||  |  ||  | ||  |   ||| ||||||||||||| ||||||||||||   ||||||||||| ||||||||||| || ||  ||||||||||||||||||| || |||||||| || ||||| || ||
------------gtaagggcgatatcaaatgtg-gtttattttgaat---atttgggatcaaatgattgctgttgtgattt---aactttatgtttttggttctt--ctttttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA

upper sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcaacattttaaaaaatttattggatgcatacttgccatgcatttgatttagccttgctttgttactgccactacttaaaaatttggtaattcagttttcttattttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTGAATGGTGATGCTGCTGCCTTGATGATTCGAGA
    | |  ||  ||| ||||     |||   |||      ||   ||| | |     | | |||  |  ||  | |     |  ||||||  ||| |||| |           |||||||| || |||||||| |||   |||||||| |||||||||||||| || ||| | |||||||||||||||||||| || ||||| |||||||| || ||
----gtatgatcataacaaat-----ggaacaatatacaagatagttttaactcctgttagtttttgttatgttaat----tatgatttgg--atttagttat-----------tcagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGA

upper sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S161_122V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagcaacattttaaaaaatttattggatgcatacttgccatgcatttgatttagccttgctttgttactgccactacttaaaaatttggtaattcagttttcttattttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTGAATGGTGATGCTGCTGCCTTGATGATTCGAGA
           | |||  | |  ||  ||     | ||      |  ||  |      |||    ||         ||  | | | | || |   |  ||    | |||  | | |||||||  | ||||| || || || ||  | ||||| ||  | || ||||| ||| |  | ||||| ||||||||||| |||||||| |||||||| |||||
-----------tctaatcagtgaatgtgaaatggagttattgaactcttagtcatcttttgaacggtag-----ggtaacttacagtgtgttttatttgtggcttgatt--catgcagACCTCATCAATGTATTCGAAGTCTTCTTGCCTCAGCTCTTACTCTACCCTAATCCTACCGATCCTTTGAATGGTGAAGCTGCTGCGTTGATGATGCGAGA

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|58017503|gb|CX704245.1|CX704245
EST:     TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTG                         ACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
genomic: TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTGgtaagcaaca ... tttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
EST: gi|298184362|gb|HO029575.1|HO029575
EST:     TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTG                         ACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
genomic: TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTGgtaagcaaca ... tttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
EST: gi|22931743|gb|BU548882.1|BU548882
EST:     TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTG                         ACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
genomic: TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTGgtaagcaaca ... tttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
EST: gi|298182712|gb|HO031447.1|HO031447
EST:     TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTG                         ACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
genomic: TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTGgtaagcaaca ... tttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
EST: gi|151394328|gb|EV264199.1|EV264199
EST:     TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTG                         ACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
genomic: TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTGgtaagcaaca ... tttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
EST: gi|298183606|gb|HO028819.1|HO028819
EST:     TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTG                         ATCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA
genomic: TGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTGgtaagcaaca ... tttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttactgccactacttaaaaatttggtaattcagttttcttattttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTGAATGGTGATGCTGCTGCCTTGATGATTCGAGA
                               ttcagttttcttattt  CT-rich tract
                ttaaaaatttggtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaacattttaaaaaatttattggatgcatacttgccatgcatttgatttagccttgctttgttactgccactacttaaaaatttggtaattcagttttcttattttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTGAATGGTGATGCTGCTGCCTTGATGATTCGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC