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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatctcactttatatctcctacttcacagcattagaaatctttctggataatactatctggaatttaccttgatcatgagtcctttttatttttgtttctgatatgttatgtgtaaccatgtactgtctttgtgccaacagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATAAATGCTATCGTTAAAGTATTAGAGTTAGCTTTGAAG

Basic information

species Glycine max
transcript GLYMA20G33910.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgatctcactttatatctcctacttcacagcattagaaatctttctggataatactatctggaatttaccttgatcatgagtcctttttatttttgtttctgatatgttatgtgtaaccatgtactgtctttgtgcca-acagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATAAATGCTATCGTTAAAGTATTAGAGTTAGCTTTGAAG
| ||| || | | | | ||| || ||| || || |||| || | || || | | ||||||| || |||||||||||| | ||||| || ||||| ||||||||||| || |||| || ||||| || ||||| ||| |||||
------------------------------------------------------------gtaagttttttactccctgctcaattaagtttcttgatgtgtcatatcaattatagaagttactgaattggaattaatctatgtagGAACTAGACGATCCTCTCATTCTTATCCACGAGAAGAAGATCTCAAGCATCAACTCTATAGTGAAAGTGTTGGAGTTGGCTCTGAAG
















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|19053143|gb|BM731810.1|BM731810
EST:     GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGT                         GAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATA
genomic: GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGTgtatgatctc ... gtgccaacagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATA
EST: gi|208046164|gb|GD848664.1|GD848664
EST:     GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGT                         GAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATA
genomic: GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGTgtatgatctc ... gtgccaacagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATA
EST: gi|16281494|gb|BI944516.1|BI944516
EST:     GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGT                         GAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATA
genomic: GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGTgtatgatctc ... gtgccaacagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATA
EST: gi|16277971|gb|BI942659.1|BI942659
EST:     GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGT                         GAACTTGAGGATCCTCTCATTATAATCCATGANAAGAAAATCTCAAGCATA
genomic: GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGTgtatgatctc ... gtgccaacagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATA
EST: gi|207844823|gb|GD816660.1|GD816660
EST:     GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGT                         GAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAAATCTCAAGCAT
genomic: GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGTgtatgatctc ... gtgccaacagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAA-TCTCAAGCAT
EST: gi|16284788|gb|BI946271.1|BI946271
EST:     GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGT                         GAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATA
genomic: GGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGAAATGTgtatgatctc ... gtgccaacagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttttgtttctgatatgttatgtgtaaccatgtactgtctttgtgccaacagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATAAATGCTATCGTTAAAGTATTAGAGTTAGCTTTGAAG
                        gtgtaac  putative branch site (score: 3)
 tctttgt  putative PPT
 atatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatctcactttatatctcctacttcacagcattagaaatctttctggataatactatctggaatttaccttgatcatgagtcctttttatttttgtttctgatatgttatgtgtaaccatgtactgtctttgtgccaacagGAACTTGAGGATCCTCTCATTATAATCCATGAAAAGAAAATCTCAAGCATAAATGCTATCGTTAAAGTATTAGAGTTAGCTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG