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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttaatgttttctatttgagtattggattttgtgtactgttgtattaatcattggggtatactattcattttcctgatttattgacatctctttgtagGAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAGTTACACCTTTCAAAGCAGGGAAAGAAGCAG

Basic information

species Glycine max
transcript GLYMA12G07590.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G07590.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G60410.2 (Arabidopsis thaliana), 3'ss of exon 2
----cttttaatgttttctatttgagtattggattttgtgtactgttgtattaatcattggggtatactattcattttcctgatttattgacatctctttgtagGAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAGTTACACCTTTCAAAGCAGGGAAAGAAGCAG
    ||  ||| | |||    ||  |  | |   ||  |||  | ||| ||| |   |||   ||   ||  | |     ||  || |||   |   || | |||||||| |    |||||||| |||||||||||||| ||||||||||||||| |    ||||| || |||||||||||||||
ttatctcataagggttttggattatggttcgtggttgctgt--tattgaatttagtcttgctcta-gttaagcttaacgttgtgtttttgttgtgggtt-gcagGAAAAACTTTCATATTTTCGGATAAAAGAGCTCAAGGATGTGCTCACTCAGCTGGGACTTTCGAAACAGGGAAAGAAGCAG
















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|120532141|gb|EH260274.1|EH260274
EST:     CGGGCAGAATTTTTGGGTTTGACGGCATGGATTTGGTACCGAGCGTCAAG                         GAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAG
genomic: CGGGCAGAATTTTTGGGTTTGACGGCATGGATTTGGTACCGAGCGTCAAGgtatacgatt ... ctctttgtagGAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAG
EST: gi|209727434|gb|BW663720.1|BW663720
EST:     CGGGCAGAATTTTTGGGTTTGACGGCATGGATTTGGTACCGAGCGTCAAG                         GAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAG
genomic: CGGGCAGAATTTTTGGGTTTGACGGCATGGATTTGGTACCGAGCGTCAAGgtatacgatt ... ctctttgtagGAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAG
EST: gi|209696512|gb|BW666889.1|BW666889
EST:     CGGGCAGAATTTTTGGGTTTGACGGCATGGATTTGGTACCGAGCGTCAAG                         GAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAG
genomic: CGGGCAGAATTTTTGGGTTTGACGGCATGGATTTGGTACCGAGCGTCAAGgtatacgatt ... ctctttgtagGAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAG
EST: gi|209719159|gb|BW679752.1|BW679752
EST:     CGGGCAGAATTTTTGGGTTTGACGGCATGGATTTGGTACCGAGCGTCAAG                         GAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAG
genomic: CGGGCAGAATTTTTGGGTTTGACGGCATGGATTTGGTACCGAGCGTCAAGgtatacgatt ... ctctttgtagGAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatcattggggtatactattcattttcctgatttattgacatctctttgtagGAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAGTTACACCTTTCAAAGCAGGGAAAGAAGCAG
                                    tattgac  putative branch site (score: 2)
                                          catctcttt  CT-rich tract
              tatactattcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttaatgttttctatttgagtattggattttgtgtactgttgtattaatcattggggtatactattcattttcctgatttattgacatctctttgtagGAAAAATTAAACTATTTTCGTATAAAAGAGCTCAAAGATGTGCTCACTCAGTTACACCTTTCAAAGCAGGGAAAGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - tgtgtac
- - - - - - - - - - - - - - - - - - - -tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttggggt