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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGTTTCAGCGTCGAGCGAAAAGAAGATTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactaccgatcaaactctcttttcagctaaaaatttagtttccgtttctgagtgaccaatggttgcttttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G09340.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09340.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os12g23180.1 (Oryza sativa), 5'ss of exon 2
-CTATGTTTCAGCGTCGAGCGAAAAGAAGATTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgt---tccactaccgatcaaactctcttttcagctaaaaatt---tagtttccgtttctgagtgaccaatggttgcttttgcag-------------
  || |   ||||  |   |   ||||| |||||  | ||||| || ||  | ||||||||| | |||||||||||| |||||||||| ||||| || |||||   ||   |    |      | | |||||  ||  || |    || |||| || | |  | ||   |  |||  ||    |              
GGTA-GCAGCAGCTGCAGACTCCAAGAACATTCTTGTGATGGGGGGAACCAGGTTCATTGGTGTCTTCTTGTCCAGGCTCCTTGTCAAGGAGGGGCACCAGgtatgtcagttgtgtagtgtgatattttttcccctgtaagtacaatattttctgtgttttggagaagta-agttaattgaaaaactgtatttgttag
















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|124861312|gb|EH945749.1|EH945749
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGG
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGG
EST: gi|124906833|gb|EH980913.1|EH980913
EST:     TTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGG-TAAATCTCCCTATTGCCAAACAATTGCCCGG
genomic: TTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCC-TATTGCCAAACAATTGCCCGG
EST: gi|164154146|gb|ES092173.1|ES092173
EST:     TTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
genomic: TTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
EST: gi|125288413|gb|EL302498.1|EL302498
EST:     TTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
genomic: TTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
EST: gi|125201788|gb|EL216742.1|EL216742
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAA
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAA
EST: gi|124812323|gb|EH897189.1|EH897189
EST:     TCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
genomic: TCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
EST: gi|124717278|gb|EH808680.1|EH808680
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCCTCTTATTGCCAAACAATTGCCCGG
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATC-TCCTATTGCCAAACAATTGCCCGG
EST: gi|124751868|gb|EH841998.1|EH841998
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCTCTTATTGCCAAACAATTGCCCGGT
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
EST: gi|124953491|gb|EL028669.1|EL028669
EST:     TTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG-CNTCAG                         GTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
genomic: TTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
EST: gi|116412032|gb|EG454624.1|EG454624
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
EST: gi|125051166|gb|EL123435.1|EL123435
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCTCCT
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCT
EST: gi|124785698|gb|EH875377.1|EH875377
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAAT
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAAT
EST: gi|125280704|gb|EL294789.1|EL294789
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGG
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGG
EST: gi|116412031|gb|EG454623.1|EG454623
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGT
EST: gi|125283666|gb|EL297751.1|EL297751
EST:     GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAG                         GTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAA
genomic: GATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactac ... gcttttgcagGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGTTTCAGCGTCGAGCGAAAAGAAGATTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGGACATCAGgttccactaccgatcaaactctcttttcagctaaaaatttagtttccgtttctgagtgaccaatggttgcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG