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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCCTTAAGTTCATCTTTGTGGTGAACTTCCTTACGTATCTCTGTGTTTTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCTgtaagtaacctaccaccttacacataccaagtgtctactgcttgtttattttccttctcttacttaagtatgaagggggatgtccccattatgaaaattt...

Basic information

species Arabidopsis thaliana
transcript AT3G07950.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G07950.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G07160.2 (Glycine max), 5'ss of exon 4
AGTTCCTTAAGTTCATCTTTGTGGTGAACTTCCTTACGTATCTCTGTGTTTTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCTgtaagtaacctaccaccttacacataccaagtgtctactgcttgtttattttccttctcttacttaagtatgaagggggatgtccccattatgaaaattt------
| ||| |||| || ||||||||||| ||  | || || |   | ||| | ||| | || || ||||||||||||||||| || ||||||||   |||||||||||||   ||  | |    |||  |  || |  || |     ||  || | || ||| |  | |  | | |         | |  | ||| | | ||       
AATTCTTTAAATTTATCTTTGTGGTTAATCTTCTAACTTCAGTATGTTTATTCATCACTGCTATTGCCTTATACTACATTACAAGGCTGGAGACTTACCTgtaagta-tataaaatccattacaatctgagaggatatt-----ttctttctgctgctcatgatgatttgtcatatttttctttcagagtattatatttctccctt
















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|301501412|gb|HO206952.1|HO206952
EST:     TTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCT                         ATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGCAGGCCTTCTTGTACG
genomic: TTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCTgtaagtaacc ... tcctggctagATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGCAGGCCTTCTTGTAGG
EST: gi|163969010|gb|ES008060.1|ES008060
EST:     AGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCT                         ATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGCAGGCCTTCTTGTAGG
genomic: AGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCTgtaagtaacc ... tcctggctagATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGCAGGCCTTCTTGTAGG
EST: gi|125192972|gb|EL207926.1|EL207926
EST:     TTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCT                         ATATATGCCCTTTGCTTGGTTTTC
genomic: TTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCTgtaagtaacc ... tcctggctagATATATGCCCTTTGCT-GGTTTTC
EST: gi|164134655|gb|ES055701.1|ES055701
EST:     TTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCT                         ATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGCAGG
genomic: TTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCTgtaagtaacc ... tcctggctagATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGCAGG
EST: gi|163984985|gb|ES012222.1|ES012222
EST:     AGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCT                         ATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGCAGGCCTTCTTGTAGG
genomic: AGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCTgtaagtaacc ... tcctggctagATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGCAGGCCTTCTTGTAGG
EST: gi|124798913|gb|EH888592.1|EH888592
EST:     TTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCT                         ATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGC
genomic: TTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCTgtaagtaacc ... tcctggctagATATATGCCCTTTGCTGGTTTTCATGGTGTCTTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTCCTTAAGTTCATCTTTGTGGTGAACTTCCTTACGTATCTCTGTGTTTTCGTTACAGCCATTGCCTTATACTACATAACGAGGCTGGAAGTTTACCTgtaagtaacctaccaccttacacataccaagtgtctactgcttgtttattttccttctcttacttaagtatgaagggggatgtccccattatgaaaattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgaaaa