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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcatactccactgaacaatagttgcataaatagttgctatccattgtttggaaaattctataaccttctttttgtaatctatttttctttctgtaacagTGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGG

Basic information

species Arabidopsis thaliana
transcript AT1G61250.2
intron # 9
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|125019465|gb|EL091734.1|EL091734
EST:     GTCTTTGCTGCAGTTGCTCCACCTGTCGTCTTCAAAGGAAAATCTCTTGC                         TGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGGA
genomic: GTCTTTGCTGCAGTTGCTCCACCTGTCGTCTTCAAAGGAAAATCTCTTGCgtaagtttct ... tctgtaacagTGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGGA
EST: gi|124793949|gb|EH883628.1|EH883628
EST:     TTGCTCCACCTGTCGTCTTCAAAGGAAAATCTCTTGC                         TGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGG
genomic: TTGCTCCACCTGTCGTCTTCAAAGGAAAATCTCTTGCgtaagtttct ... tctgtaacagTGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGG
EST: gi|125208102|gb|EL223056.1|EL223056
EST:     CCTGTCGTCTTCAAAGGAAAATCTCTTGC                         TGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGG-
genomic: CCTGTCGTCTTCAAAGGAAAATCTCTTGCgtaagtttct ... tctgtaacagTGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGG
EST: gi|125031336|gb|EL103605.1|EL103605
EST:     GTTGCTCCACCTGTCGTCTTCAAAGGAAAATCTCTTGC                         TGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGG
genomic: GTTGCTCCACCTGTCGTCTTCAAAGGAAAATCTCTTGCgtaagtttct ... tctgtaacagTGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttggaaaattctataaccttctttttgtaatctatttttctttctgtaacagTGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGG
             ctataac  putative branch site (score: 3)
                   ccttctttttgtaatc  CT-rich tract
                        tttttgtaatctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcatactccactgaacaatagttgcataaatagttgctatccattgtttggaaaattctataaccttctttttgtaatctatttttctttctgtaacagTGGGATCTTACCTGCAATAGATGTCTTAAGTGGTCAAGCAATTGTTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- catactc
- - - - - - - aacaata
- - - - - - - - - - - - gcataaa
- - - - - - - - - - - - - - - - - - - - - - -tgtttgg