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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtttccttctcatcaatgatcaatgatataatctcgatcatttggtaataatgtgtccaattttgtattcagGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGCCTTAGCGCATAGAATAGCTGCTGTAGGAACTGGTTCAAGACCATTGCTA

Basic information

species Arabidopsis thaliana
transcript AT4G39540.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39540.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G15160.1 (Glycine max), 3'ss of exon 4
--------------------------------------------gtgcgtttccttctcatcaatgatcaa-tgatataatctcgatcatttggtaataatgtgtccaattttgtattcagGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGCCTTAGCGCATAGAATAGCTGCTGTAGGAACTGGTTCAAGACCATTGCTA----------------
                                              |  || ||  | | |     || || |  | | |  |   || |     ||  || | |   | ||   ||    ||| || |||||  | |  |||||| ||||| | |||||||||||| |||||||||  || |||||| | ||||||||||||| |||  | ||| | |||                
gtgaggcccatcaattggtataacaattaacatgttaatgagaaaagttttaccaccacttttgccattaactcttctcacttgagtcttcacacaaacatatatatgaattgccat----gaaatatatgcaccagGAAATTAGTGTTTGGTTGGATGTACCTCTAAAAGCCTTAGGTCAGAGAATAACAGCTGTAGGAACTGATTCTCGCCCACTTCTACATTATGAAGAAGGTG

upper sequence: AT4G39540.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G39710.1 (Glycine max), 3'ss of exon 4
-------------------------gtgcgtttccttctcatcaatgatcaatgatataatctcgatcatttggtaataatgtgtcc--aattttgtatt--cagGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGCCTTAGCGCATAGAATAGCTGCTGTAGGAACTGGTTCAAGACCATTGCTA
                             ||||   |  | || |   |      || | |||      ||| || || | |  | |  |  | || |||  |||||| || |||||  | || |||||| ||||| | ||||||||| |||||||||| || || |||||| | ||||||||||||| |||  ||||| | |||
gtataataattaacatactaatgagaaaagttttaattacctccacttttgccatta-actcttctcactttagtcatcacgcatacttatatatggattgccagGAAATATATGCAGCAGGGGATTAGTGTTTGGTTGGATGTACCTGTAGAAGCCTTGGCTCAGAGAATAACAGCTGTAGGAACTGATTCTCGACCACTTCTA
















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|125309796|gb|EL323881.1|EL323881
EST:     CAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTG                         GAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGC
genomic: CAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTGgtgcgtttcc ... ttgtattcagGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGC
EST: gi|164214916|gb|ES041749.1|ES041749
EST:     AAGTTGTTGTTTCAACCGGGGGGAGGGGCAGTTATAAGACCCATCAATTG                         GAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGC
genomic: AAGTTGTTGTTTCAACC-GGGGGAGGGGCAGTTATAAGACCCATCAATTGgtgcgtttcc ... ttgtattcagGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGC
EST: gi|86084950|gb|DR380709.1|DR380709
EST:     CAAGTTGTTGTTTCAACCGGGGGAGGGGCAGTTATAAGACCCWTCAATTG                         GAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGC
genomic: CAAGTTGTTGTTTCAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTGgtgcgtttcc ... ttgtattcagGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGC
EST: gi|125275307|gb|EL289392.1|EL289392
EST:     TTGTTGTTTCAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTG                         GAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGCACCTCTAGAAGC
genomic: TTGTTGTTTCAACCGGGGGAGGGGCAGTTATAAGACCCATCAATTGgtgcgtttcc ... ttgtattcagGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcaatgatataatctcgatcatttggtaataatgtgtccaattttgtattcagGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGCCTTAGCGCATAGAATAGCTGCTGTAGGAACTGGTTCAAGACCATTGCTA
                                         aattttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtttccttctcatcaatgatcaatgatataatctcgatcatttggtaataatgtgtccaattttgtattcagGAAGTACATGCATAAAGGTATTAGTATTTGGCTTGATGTACCTCTAGAAGCCTTAGCGCATAGAATAGCTGCTGTAGGAACTGGTTCAAGACCATTGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT