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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctttacgtacattggcttgtgttgattacaatccaagcttgtgcagttgtgtattgtttcttagtgatgttgtgtactgggtggggctttacttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAATGCTATCTTCTGTTTCAAGTTCAGAACTCACTTTGGAGGTGGTAAATCTT

Basic information

species Arabidopsis thaliana
transcript AT5G28060.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28060.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0030g01620.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------gtatgttctttacgta-cattggcttgtgttgattacaatccaagcttgtgcagttgtgtattgtttcttagtgatgttgtgtactgggtggggctttacttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAATGCTATCTTCTGTTTCAAGTTCAGAACTCACTTTGGAGGTGGTAAATCTT
                                |||  | |  |  |  ||||||  | ||| | ||  | |  |   ||||||| || | || ||  |  |     ||||||  | ||  ||    |||  |||  ||||||||||| | ||||| ||| |||| || ||||||||||| ||||| || ||| | || ||   |||||||||| | ||||||||||||||||| || ||| 
gtaatctccgcaatctcccttcagtattttattatcatttgaaaatttcattggtctttgt-gcttgtagtttatatttgtgcatttctatagtgcctgct--ctgtgttgtagagtgattgattatttgtttg--tgaagGCTGAGTTGAAGGATAAACTGGCAAGCATGTATGAGGTGAAGGATCCCAATTCAATTTTTGTTTTCAAGTTCCGGACTCACTTTGGAGGTGGGAAGTCTA
















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|125265573|gb|EL279658.1|EL279658
EST:     CCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
genomic: CCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
EST: gi|125288234|gb|EL302319.1|EL302319
EST:     TCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
genomic: TCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
EST: gi|124753961|gb|EH844091.1|EH844091
EST:     TCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGAACCCAAA
genomic: TCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGA-CCCAAA
EST: gi|152034225|gb|BP822397.2|BP822397
EST:     GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTCTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
genomic: GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
EST: gi|164180694|gb|ES018222.1|ES018222
EST:     GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTGAAGGAGAAGTTGGCGAGG
genomic: GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGG
EST: gi|152034969|gb|BP841119.2|BP841119
EST:     GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTGTGAGGTTAAGGACCCAAAT
genomic: GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
EST: gi|164123995|gb|EL983950.1|EL983950
EST:     TATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTGAAGGAGAAGTTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
genomic: TATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
EST: gi|125084151|gb|EL144472.1|EL144472
EST:     AAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
genomic: AAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
EST: gi|125327573|gb|EL341653.1|EL341653
EST:     GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTT
genomic: GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTT
EST: gi|86084565|gb|DR380324.1|DR380324
EST:     GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
genomic: GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
EST: gi|86078425|gb|DR374182.1|DR374182
EST:     GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
genomic: GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
EST: gi|86081226|gb|DR376983.1|DR376983
EST:     GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
genomic: GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAAT
EST: gi|124942113|gb|EL018409.1|EL018409
EST:     GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAG                         GCTGAGCTTAAAGGAGAAATTGGCGAGGATGTATGAG
genomic: GTTATTGATGTTCTTCATCCTGGAAGAGCCAATGTTTCAAAGgtatgttctt ... ttgtttgaagGCTGAGCTTAA-GGAGAAATTGGCGAGGATGTATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtattgtttcttagtgatgttgtgtactgggtggggctttacttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAATGCTATCTTCTGTTTCAAGTTCAGAACTCACTTTGGAGGTGGTAAATCTT
                                       ctttactt  CT-rich tract
     attgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttctttacgtacattggcttgtgttgattacaatccaagcttgtgcagttgtgtattgtttcttagtgatgttgtgtactgggtggggctttacttgtttgaagGCTGAGCTTAAGGAGAAATTGGCGAGGATGTATGAGGTTAAGGACCCAAATGCTATCTTCTGTTTCAAGTTCAGAACTCACTTTGGAGGTGGTAAATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG