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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaattttataagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag

Basic information

species Arabidopsis thaliana
transcript AT2G27020.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 10
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaattttataagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag
||| ||     |||| |||||||| |||||||| |||||||| |||||  | ||||||||||| || || ||||| ||  |||||||||||||    || | |   |  ||    || ||  |   | |    | || ||  | |||  |    |  | | |  |  | || ||
CATTTATGGAGTACATGATGAAGCTAAGGACAAAGCTTTTGAGTTGGAATTAAGCTGGATATGTGATGAATCAAATCGCCAGCATCAGAAGgtg---ttctgttgttatttaaaaataaataa-actctgtccatatttttgtgaactttgctcacttggcatactgcatacag

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G445100_T02 (Zea mays), 5'ss of exon 10
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaattttataagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag------------
 || ||     | || |||||||| |||||||| |||||||| |||||| |||||||||| || ||||| || || ||  ||||||||||||||      |||   |  |  |  |||||| |||   |  | |  | |    |    |  |  ||  || |||| |    |              
AATTTATGCAGTGCATGATGAAGCTAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGAGGAATCGAAGCGCCAGCATCAGAAGgta-----ctatggatattcac--atgaagaatggcctctgtatgtttctccatttgaatttaaagctgaactcctttgctcacctgtcatacag

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G445100_T01 (Zea mays), 5'ss of exon 10
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaattttataagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag------------------------
 || ||     | || |||||||| |||||||| |||||||| |||||| |||||||||| || ||||| || || ||  ||||||||||||||      |||   |  |  |  |||||| |||   |  | |  | |    |    |  |  ||  || |||| |    |                          
AATTTATGCAGTGCATGATGAAGCTAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGAGGAATCGAAGCGCCAGCATCAGAAGgta-----ctatggatattcac--atgaagaatggcctctgtatgtttctccatttgaatttaaagctgaactcctttgctcacctgtcatacaggtcccaaatgac

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G028346_T01 (Zea mays), 5'ss of exon 8
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaattttataagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag---------------
 || ||     | || || ||| |||||||||| |||||||| |||||| |||||||||| || || || || || ||  ||||||||||||||   |   |  ||   || |    |||| |||   |    |  | |||   |     || ||||   ||  | || | | |               
AATTTATGGAGTGCATGACGAATCCAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtgggaccagatatt-caggcgaagaatggcctctctatgt-ttctcgatttgaatttaaagctgaaacttctt-tggtcacctgtcatacag

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G130398_T03 (Zea mays), 5'ss of exon 10
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgta---aaatttt-------ataagtgcttgcttatgaaggatgatttaaggagatattca-taaaccatatataaattggactcgtcgtatag
 || ||     | || || ||||| |||||||| |||||||| |||||| |||||||||| || || || || || ||  ||||||||||||||     || ||       | ||    |||  | || | | |  |  | | | || |  |  | |  |  | |   || |  |  | ||| ||
AATTTATGGAGTGCATGACGAAGCGAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtactgggatattcacgcggagaatgagttgtctctgtatggttctcgatgtaaatttgaagcagaaaacttttttttttgcgtacttgtacag

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv08s0040g00410.t01 (Vitis vinifera), 5'ss of exon 9
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaattttataagtgctt-gcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag----------------
||| ||   | |||||||||| |||||||||||||| ||||| ||||| ||||||||| | || ||||||||||| ||  |||||||||||||||  | ||  |  |     | | | |||  || |  | |    ||||    ||  ||| ||     | || |   |  ||                  
CATTTATGGGGTACACGATGAGGCCAAGGACAAGGCATTTGAGTTGGAAATGAGCTGGGTTTGTGAGGAGTCAAACCGCCAGCATCAGAAGgtaatctcttgaatttatcaagatcaagaaacattaacttaactcatatcttgaagacatctaccctgttgattgcacccatgctcactagctggatagc

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S72_57V6.4 (Physcomitrella patens), 5'ss of exon 11
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaa-attttat---aagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag-------------
 || ||     | || ||||| |||||||||||||| |||||  |||||||||||||||| || || |||||||| || ||||||||    ||||| |||  ||   |  |  |  | |     ||    ||     |  ||||||  ||   ||  ||  ||| ||   || ||                
TATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S72_57V6.6 (Physcomitrella patens), 5'ss of exon 11
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaa-attttat---aagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag-------------
                            |||||||| |||||  |||||||||||||||| || || |||||||| || ||||||||    ||||| |||  ||   |  |  |  | |     ||    ||     |  ||||||  ||   ||  ||  ||| ||   || ||                
----------------------------GACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S72_57V6.7 (Physcomitrella patens), 5'ss of exon 10
---------CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaa-attttat---aagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag-------------
          || ||     | || ||||| |||||||||||||| |||||  |||||||||||||||| || || |||||||| || ||||||||    ||||| |||  ||   |  |  |  | |     ||    ||     |  ||||||  ||   ||  ||  ||| ||   || ||                
ACATTTCAGTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGAgtaaatattccatcctacattttccccttctctggtctcttgtgttacctattcagcaatattaactagcttgtacgtctcctactttgtaactgcccga

upper sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ26741 (Selaginella moellendorffii), 5'ss of exon 10
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaattttataagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag
|||||||    | ||||| |||||||||||||| || |||||| |||| ||||||||||| ||||| ||||| ||    ||||| || ||||     | ||   |  ||   ||    | | |  | |       || |||  |  |    | |   ||  |            
CATCTACGGAGTTCACGACGAAGCCAAGGACAAAGCCTTTGAACTGGAAATGAGCTGGATTTGCGACGAGTCGAACAAGGAGCACCAAAAGg-----tcttgccatcgcactctcgctacgtactagtccctcgtattttctaatgcttgttttgctttccag-----------

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|47830869|gb|CK120553.1|CK120553
EST:     AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAG                         GTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
genomic: AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaatttt ... cgtcgtatagGTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
EST: gi|86034506|gb|DR330259.1|DR330259
EST:     AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAG                         GTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
genomic: AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaatttt ... cgtcgtatagGTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
EST: gi|116417246|gb|EG459838.1|EG459838
EST:     AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAG                         GTCCCTGATGATTTTTTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
genomic: AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaatttt ... cgtcgtatagGTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
EST: gi|164128528|gb|ES027058.1|ES027058
EST:     AATTGGAGATGAGCTGGATATGCGAGGAGTC-AAACGAGAGCATCAGAAG                         GTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCA
genomic: AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaatttt ... cgtcgtatagGTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCA
EST: gi|47830430|gb|CK120114.1|CK120114
EST:     AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAG                         GTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGNAGCTAAAACTGCGCTC
genomic: AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaatttt ... cgtcgtatagGTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
EST: gi|116417245|gb|EG459837.1|EG459837
EST:     AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAG                         GTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
genomic: AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaatttt ... cgtcgtatagGTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
EST: gi|125045494|gb|EL117763.1|EL117763
EST:     CTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAG                         GTCCCTGATGATCTTCTGGAAGAAGCAAAAGACGGCAGCTAAAACTGCGCT
genomic: CTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaatttt ... cgtcgtatagGTCCCTGATGATCTTCTGGAAGAAGCAAA-GACGGCAGCTAAAACTGCGCT
EST: gi|86075611|gb|DR371368.1|DR371368
EST:     AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAG                         GTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC
genomic: AATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaatttt ... cgtcgtatagGTCCCTGATGATCTTCTGGAAGAAGCAAAGACGGCAGCTAAAACTGCGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaattttataagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag

- - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA