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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatcgccgcacatgttttaaaacagagtcatgtaaaccctcatccatgtctgataaattttctctgggatatctgttaatgaatttaaaatatttacagGTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGTATCGGAAACAACAAGAGGACGCGTCAACGAACCAGTACTGTCAGTACGA

Basic information

species Arabidopsis thaliana
transcript AT1G11260.1
intron # 1
splice site 3'
intron type U2

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|152035146|gb|BP846204.2|BP846204
EST:     TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCG                         GTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
genomic: TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCGgttagtgtct ... atatttacagGTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
EST: gi|124710328|gb|EH801730.1|EH801730
EST:     CTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCG                         GTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
genomic: CTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCGgttagtgtct ... atatttacagGTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
EST: gi|164134600|gb|ES030852.1|ES030852
EST:     TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCG                         GTGGTGTGACGTCGATGCCGTCTTTCC
genomic: TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCGgttagtgtct ... atatttacagGTGGTGTGACGTCTATGCCGTCTTTCC
EST: gi|152033951|gb|BP820967.2|BP820967
EST:     TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCG                         GTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
genomic: TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCGgttagtgtct ... atatttacagGTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
EST: gi|301502820|gb|HO208360.1|HO208360
EST:     TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCG                         GTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
genomic: TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCGgttagtgtct ... atatttacagGTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
EST: gi|152034748|gb|BP836052.2|BP836052
EST:     GGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCG                         GTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
genomic: TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCGgttagtgtct ... atatttacagGTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
EST: gi|152035099|gb|BP844538.2|BP844538
EST:     TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCG                         GTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT
genomic: TGTTGCTGCCATGGGCGGTCTCATCTTCGGATACGATATCGGAATCTCCGgttagtgtct ... atatttacagGTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtctgataaattttctctgggatatctgttaatgaatttaaaatatttacagGTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGTATCGGAAACAACAAGAGGACGCGTCAACGAACCAGTACTGTCAGTACGA
                             tgttaat  putative branch site (score: 3)
                        atatctgttaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatcgccgcacatgttttaaaacagagtcatgtaaaccctcatccatgtctgataaattttctctgggatatctgttaatgaatttaaaatatttacagGTGGTGTGACGTCTATGCCGTCTTTCCTCAAGCGATTCTTCCCGTCGGTGTATCGGAAACAACAAGAGGACGCGTCAACGAACCAGTACTGTCAGTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - ccgcaca
- - - - - - - - - - aaacaga
- - - - - - - - - - - - - - - - -taaaccc
- - - - - - - - - - - - - - - - - - - - tcatcca