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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacactttcatagtctctgttattttttgcttcaagctacactgttattggcttacctcaagctatgcaatgagtattcattgaaatggtttcgattggttttgcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G27400.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ26852 (Selaginella moellendorffii), 3'ss of exon 1
gtaagaacactttcatagtctctgttattttttgcttcaagctacactgttattggcttacctcaagctatgcaatgagtattcattgaaatggtttcgattggttttgcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
                                                          |   | ||  |  |||| | |   || ||||      |  | |||| ||   | | ||||||||||||||||||||  |||||||| ||||||||||||||
---------------------------------------------------------gtgagtgaaatt-cgcaa-gcgctctcgttgac----ctcagcttggatt---gatcgcagCTTGCAAGGCGAGAGGCTCCGATCTCCGGGTCCACTTCAAG

upper sequence: AT1G27400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ21308 (Selaginella moellendorffii), 3'ss of exon 1
gtaagaacactttcatagtctctgttattttttgcttcaagctacactgttattggcttacctcaagctatgcaatgagtattcattgaaatggtttcgattggttttgcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
                                                          |   | ||  |  |||| | |   || ||||      |  | |||| ||   | | ||||||||||||||||||||  |||||||| ||||||||||||||
---------------------------------------------------------gtgagtgaaatt-cgcaa-gcgctctcgttgac----ctctgcttggatt---gatcgcagCTTGCAAGGCGAGAGGCTCCGATCTCCGGGTCCACTTCAAG
















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|164229631|gb|ES057186.1|ES057186
EST:     GAAGTACTCTCAAGAGCCCGATAATATCACCAAAAT                         CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
genomic: GAAGTACTCTCAAGAGCCCGATAATATCACC-AAATgtaagaacac ... gcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
EST: gi|47827860|gb|CK117544.1|CK117544
EST:     GTGAAGTACTCTCAAGAGCCCGATAATATCACCAAAT                         CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
genomic: GTGAAGTACTCTCAAGAGCCCGATAATATCACCAAATgtaagaacac ... gcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
EST: gi|124823160|gb|EH908026.1|EH908026
EST:     AAGTACTCTCAAGAGCCCGTATAATATCACCAAAT                         CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
genomic: AAGTACTCTCAAGAGCCCG-ATAATATCACCAAATgtaagaacac ... gcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
EST: gi|86074318|gb|DR370075.1|DR370075
EST:     CGATAATATCACCAAAT                         CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
genomic: CGATAATATCACCAAATgtaagaacac ... gcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
EST: gi|163982884|gb|ES002582.1|ES002582
EST:     GAAGTACTCTCAAGAGCCCGATAATATCACCAAAT                         CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
genomic: GAAGTACTCTCAAGAGCCCGATAATATCACCAAATgtaagaacac ... gcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
EST: gi|116444090|gb|EG486682.1|EG486682
EST:     GTGAAGTACTCTCAAGAGCCCGATAATATCACCAAAT                         CTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
genomic: GTGAAGTACTCTCAAGAGCCCGATAATATCACCAAATgtaagaacac ... gcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagctatgcaatgagtattcattgaaatggtttcgattggttttgcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG
                tattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacactttcatagtctctgttattttttgcttcaagctacactgttattggcttacctcaagctatgcaatgagtattcattgaaatggtttcgattggttttgcgtttgcagCTTGCAAGGCGAGAGGAGCCGATCTCAGGGTCCACTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG