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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtctgatttctggttcttctttcgaaatattgttacttgacgtgttatgtgttgaatggttcacttggtcttgcaaaactgatatatcttgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTGAAAGAGCAAGGAGTCAAAGGCTTTTTCCGTGGATGGGTTCCTACTCTTT

Basic information

species Arabidopsis thaliana
transcript AT5G14040.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G14040.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0068g01260.t01 (Vitis vinifera), 3'ss of exon 1
-ggtctgat---ttctggttcttctttcgaaatattgttacttgacgtgttatgtgttgaatggttcacttggtcttgcaaaactgatatatcttgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTGAAAGAGCAAGGAGTCAAAGGCTTTTTCCGTGGATGGGTTCCTACTCTTT
   ||  |    ||||      |||   |||    | ||| |||  ||||||     ||   ||      || |||   |||| ||| ||   || || |  ||||||| || || |||||||||||||| |||||||| |||||| |||||||||| ||||| ||||| |  || |||||| | || ||||| ||||| ||  
ttttccaacaccttctcaacaatctaaagaagagattttatttg-tgtgttaaaaaatgttaggaaggagtgatct---aaaattgagattattttttgtttagATTGACCCTGCAAAGTACAAGAGCATTTCGTCTGGATTTGGAGTTTTGCTGAAGGAGCAGGGAGTTAGGGGATTTTTCAGGGGTTGGGTGCCTACCCTGC
















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|47831554|gb|CK121238.1|CK121238
EST:     TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAG                         ATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
genomic: TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAGgtatgtaacc ... tgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
EST: gi|164130863|gb|ES172192.1|ES172192
EST:     TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAG                         ATTGATCCAGCGAAGTACAAGAGCATC
genomic: TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAGgtatgtaacc ... tgttatccagATTGATCCAGCGAAGTACAAGAGCATC
EST: gi|116450593|gb|EG493185.1|EG493185
EST:     TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAG                         ATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
genomic: TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAGgtatgtaacc ... tgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
EST: gi|116407737|gb|EG450329.1|EG450329
EST:     TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAG                         ATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
genomic: TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAGgtatgtaacc ... tgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
EST: gi|47829640|gb|CK119324.1|CK119324
EST:     TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAG                         ATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
genomic: TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAGgtatgtaacc ... tgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
EST: gi|47829559|gb|CK119243.1|CK119243
EST:     TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAG                         ATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
genomic: TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAGgtatgtaacc ... tgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
EST: gi|125270359|gb|EL284444.1|EL284444
EST:     TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAG                         ATTGATCCAGCGAAGTA
genomic: TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAGgtatgtaacc ... tgttatccagATTGATCCAGCGAAGTA
EST: gi|47827833|gb|CK117517.1|CK117517
EST:     TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAG                         ATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG
genomic: TTACTCACATGACCGTGACTCCTCTCGATCTCGTCAAGTGCAATATGCAGgtatgtaacc ... tgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgtgttgaatggttcacttggtcttgcaaaactgatatatcttgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTGAAAGAGCAAGGAGTCAAAGGCTTTTTCCGTGGATGGGTTCCTACTCTTT
                                aactgat  putative branch site (score: 3)
                                          tcttgtt  putative PPT
                                     atatatcttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtctgatttctggttcttctttcgaaatattgttacttgacgtgttatgtgttgaatggttcacttggtcttgcaaaactgatatatcttgttatccagATTGATCCAGCGAAGTACAAGAGCATCTCGTCTGGTTTTGGAATTTTGCTGAAAGAGCAAGGAGTCAAAGGCTTTTTCCGTGGATGGGTTCCTACTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaact