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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtttaatgataagaactcaaaactcaaaagcgattttgttaagagcatttgacataattttccctgtaatgtgtagGTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATGATGGATCATTTCGGTCTCTAGCCCTAAACATTTTCAACCGCTGCAATTA

Basic information

species Arabidopsis thaliana
transcript AT4G25770.1
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|116396432|gb|EG439024.1|EG439024
EST:     TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAG                         GTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATG
genomic: TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAGgcaagtttaa ... taatgtgtagGTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATG
EST: gi|116396433|gb|EG439025.1|EG439025
EST:     TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAG                         GTGAAAACATATTGATTACATTCTGATGGCAAAGATGTTGTCTTCCACATG
genomic: TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAGgcaagtttaa ... taatgtgtagGTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATG
EST: gi|116396435|gb|EG439027.1|EG439027
EST:     TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAG                         GTGAAAACATATTGATTACATTTTGATGGCAAAGATGTTGTTTTCCACATG
genomic: TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAGgcaagtttaa ... taatgtgtagGTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATG
EST: gi|116396440|gb|EG439032.1|EG439032
EST:     TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAG                         GTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATG
genomic: TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAGgcaagtttaa ... taatgtgtagGTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATG
EST: gi|116396437|gb|EG439029.1|EG439029
EST:     TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAG                         GTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATG
genomic: TCAGCTTTCACAATAGCAAGCAACGATACGTCGCGCATAGTACCATCCAGgcaagtttaa ... taatgtgtagGTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcaaaagcgattttgttaagagcatttgacataattttccctgtaatgtgtagGTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATGATGGATCATTTCGGTCTCTAGCCCTAAACATTTTCAACCGCTGCAATTA
                         atttgac  putative branch site (score: 4)
                                    ttttccctgt  putative PPT
                         atttgacataatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtttaatgataagaactcaaaactcaaaagcgattttgttaagagcatttgacataattttccctgtaatgtgtagGTGAAAACATATTGGTTACATTCTGATGGCAAAGATGTTGTCTTCCACATGATGGATCATTTCGGTCTCTAGCCCTAAACATTTTCAACCGCTGCAATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA