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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctggcctctattttgcaacctgttgcacaatctttttttttttttttttttgtttattgatgaaacatatgtagttctttaaaagcaaaaggtggtgatgatatctatgaattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACAAGTACGCAATCCCCAACCCAAAGAGTGAGTGCAGCAAAGGTCTGCAACT

Basic information

species Arabidopsis thaliana
transcript AT5G14040.1
intron # 3
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 3
lower sequence: GRMZM2G118208_T01 (Zea mays), 3'ss of exon 3
gtaagttctggcctctattttgcaacctgttgcacaatctttttttttttttttttttgtttattgatgaaacatatgtagttctttaaaagcaaaaggtggtgatga-tatctatga-attttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACAAGTACGCAATCCCCAACCCAAAGAGTGAGTGCAGCAAAGGTCTGCAACT
                       |||   ||  |    ||   |  | |     | |  | |    |  |  | |||||    || |  |  |||  |    | || | | ||| ||  ||  |||||||||||||||||| ||||||| |||||| || |||||||||||| | |||||| | ||  | || || || ||     | ||||| ||    || |||||
-----------------------aac---tttgaggtgctgggtcatgtagagatataatctgcacagaagccttatgttaacctgtgcacccaa--gtccctaattactttctgtgttatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT

upper sequence: AT5G14040.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0068g01260.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttctggcctctattttgcaacctgttgcacaatctttttttttttttttttttgtttattgatgaaacatatgtagttctttaaaagcaaaaggtggtgatgatatctatgaattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACAAGTACGCAATCCCCAACCCAAAGAGTGAGTGCAGCAAAGGTCTGCAACT
          |  |||  ||  ||  ||| |  | | |   ||||||    |||   |   | || |||   |||  | | |  | ||||| ||        | ||| | | |      | | |||| || |||||||| |||||||| |||||||| |||||||||||| |||||||||| || || || |  || |||    ||||||| |||  |||||| ||
----------gtttctccttgtcatgctgatata-attggcttttttgggctttgcgtaaatgttaatgtt-cattagaaatcttataaaatca--------taatggttttt------tgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACAAGTATGCCATTCCTACTCCGAAGGACCAGTGCAGTAAAACTCTGCAGCT
















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|164094607|gb|ES101038.1|ES101038
EST:     CTTGTATAAGGGTCTTGCTCCACTCGTGGGGACGTCAGATTCCTT                         ACACTATGATGAAGTTT
genomic: CTTGTATAAGGGTCTTGCTCCACTC-TGGGGACGTCAGATTCCTTgtaagttctg ... aattttacagACACTATGATGAAGTTT
EST: gi|47831554|gb|CK121238.1|CK121238
EST:     CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT                         ACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA
genomic: CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTTgtaagttctg ... aattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA
EST: gi|116450593|gb|EG493185.1|EG493185
EST:     CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT                         ACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA
genomic: CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTTgtaagttctg ... aattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA
EST: gi|116407737|gb|EG450329.1|EG450329
EST:     CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT                         ACACTATGATGAAGTTTGCTTCCTTTGAGAC-ATTGTTGAGATGATTTACA
genomic: CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTTgtaagttctg ... aattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA
EST: gi|164111226|gb|ES195379.1|ES195379
EST:     GTCAGA-TCCTT                         ACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA
genomic: GTCAGATTCCTTgtaagttctg ... aattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA
EST: gi|124859158|gb|EH943595.1|EH943595
EST:     CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT                         ACACTATGATGAAGTTTGCTTCCTTTGAG
genomic: CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTTgtaagttctg ... aattttacagACACTATGATGAAGTTTGCTTCCTTTGAG
EST: gi|47829559|gb|CK119243.1|CK119243
EST:     CTTGTATAAGGGTCTTGCTCCCACTCTGGG-ACGTCAGATTCCTT                         ACACTATGATGAAGNTTGCTTCCTTTGAGACCATTGNTGAGATGATTTACA
genomic: CTTGTATAAGGGTCTTGCTCC-ACTCTGGGGACGTCAGATTCCTTgtaagttctg ... aattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA
EST: gi|124969172|gb|EL043093.1|EL043093
EST:     CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT                         ACACTATGATGAAGTTTGCTT
genomic: CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTTgtaagttctg ... aattttacagACACTATGATGAAGTTTGCTT
EST: gi|47827833|gb|CK117517.1|CK117517
EST:     CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTT                         ACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA
genomic: CTTGTATAAGGGTCTTGCTCCACTCTGGGGACGTCAGATTCCTTgtaagttctg ... aattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatatgtagttctttaaaagcaaaaggtggtgatgatatctatgaattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACAAGTACGCAATCCCCAACCCAAAGAGTGAGTGCAGCAAAGGTCTGCAACT
                                    atatctatgaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctggcctctattttgcaacctgttgcacaatctttttttttttttttttttgtttattgatgaaacatatgtagttctttaaaagcaaaaggtggtgatgatatctatgaattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACAAGTACGCAATCCCCAACCCAAAGAGTGAGTGCAGCAAAGGTCTGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG