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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgttctttaaaactttacccatcaaaattcacttcttcttctccttctaagcaacttctaatttcaatttctcgaatttttttgttttgtttttgcgtttgtacgaaacagTAAACAGCTTTTGGATCCAGAAGAAGTCGACGTAGTTCATGATCTCGATAAAGAACGTGGAATCTCAATTGATGATTTTAAGCTCATCAAGTTCCATATG

Basic information

species Arabidopsis thaliana
transcript AT5G48640.1
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|86054344|gb|DR350101.1|DR350101
EST:     GACGGTCTACCGGAAAAAATGGCTGCCAATTTCTGGAATTCATCTCACTA                         TAAACAGCTTTTGGATCCAGAAGAAGTCGACGTA-KTCATGATCTCGATAA
genomic: GACGGTCTACCGGAAAAAATGGCTGCCAATTTCTGGAATTCATCTCACTAgtaaatgttc ... tacgaaacagTAAACAGCTTTTGGATCCAGAAGAAGTCGACGTAGTTCATGATCTCGATAA
EST: gi|124765949|gb|EH856079.1|EH856079
EST:     GACGGTCTACCGGAAAAAATGGCTGCCAATTTCTGGAATTCATCTCACTA                         TAAACAGCTTTTGGATCCAGAAGAAGTCGACGTAGTTCATGATCT
genomic: GACGGTCTACCGGAAAAAATGGCTGCCAATTTCTGGAATTCATCTCACTAgtaaatgttc ... tacgaaacagTAAACAGCTTTTGGATCCAGAAGAAGTCGACGTAGTTCATGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaatttcaatttctcgaatttttttgttttgtttttgcgtttgtacgaaacagTAAACAGCTTTTGGATCCAGAAGAAGTCGACGTAGTTCATGATCTCGATAAAGAACGTGGAATCTCAATTGATGATTTTAAGCTCATCAAGTTCCATATG
 ttctaat  putative branch site (score: 2)
                  aatttttttgttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgttctttaaaactttacccatcaaaattcacttcttcttctccttctaagcaacttctaatttcaatttctcgaatttttttgttttgtttttgcgtttgtacgaaacagTAAACAGCTTTTGGATCCAGAAGAAGTCGACGTAGTTCATGATCTCGATAAAGAACGTGGAATCTCAATTGATGATTTTAAGCTCATCAAGTTCCATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA