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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctggcactatgaattgcttattgttgtcatgttacacatgtcgttttcatcttaacgaatgcattcttctctgcagCTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACC

Basic information

species Arabidopsis thaliana
transcript AT5G26360.1
intron # 6
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|124831539|gb|EH915978.1|EH915978
EST:     TGCAGAAGCGTTTCTTGAGAAGAATTACCANCCCACAGTCATATGCCGAG                         CTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAA
genomic: TGCAGAAGCGTTTCTTGAGAAGAATTACCATCCCACAGTCATATGCCGAGgtatgctggc ... ttctctgcagCTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAA
EST: gi|47829135|gb|CK118819.1|CK118819
EST:     TGCAGAAGCGTTTCTTGAGAAGAATTACCATCCCACAGTCATATGCCGAG                         CTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA
genomic: TGCAGAAGCGTTTCTTGAGAAGAATTACCATCCCACAGTCATATGCCGAGgtatgctggc ... ttctctgcagCTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA
EST: gi|86058165|gb|DR353922.1|DR353922
EST:     AATTACCATCCCACAGTCATATGCCGAG                         CTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA
genomic: AATTACCATCCCACAGTCATATGCCGAGgtatgctggc ... ttctctgcagCTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA
EST: gi|86058166|gb|DR353923.1|DR353923
EST:     AATTACCATCCCACAGTCATATGCCGAG                         CTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA
genomic: AATTACCATCCCACAGTCATATGCCGAGgtatgctggc ... ttctctgcagCTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA
EST: gi|47830309|gb|CK119993.1|CK119993
EST:     TGCAGAAGCGTTTCTTGAGAAGAATTACCATCCCACAGTCATATGCCGAG                         CTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA
genomic: TGCAGAAGCGTTTCTTGAGAAGAATTACCATCCCACAGTCATATGCCGAGgtatgctggc ... ttctctgcagCTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA
EST: gi|125220926|gb|EL235011.1|EL235011
EST:     ACAGTCATATGCCGAG                         CTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA
genomic: ACAGTCATATGCCGAGgtatgctggc ... ttctctgcagCTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtcatgttacacatgtcgttttcatcttaacgaatgcattcttctctgcagCTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACC
                            tcttaac  putative branch site (score: 2)
                                        cattcttctct  putative PPT
                      ttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctggcactatgaattgcttattgttgtcatgttacacatgtcgttttcatcttaacgaatgcattcttctctgcagCTTACATCAAGGCTCTCGAAGATTCTATTGCTGTTCTTGACAAAATTGCTATGTCAATTGATATCAATGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT