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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGCTCTTAGAGAAGCATACAAAAACAAGAAGTTGTTGCCACTCGATCTCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAGgtattttgaattcagtgacatgctttgttttggtccatacttcatgactttttctctgcattggatag

Basic information

species Arabidopsis thaliana
transcript AT3G55170.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G43770.2 (Glycine max), 5'ss of exon 2
GTCTGCTCTTAGAGAAGCATACAAAAACAAGAAGTTGTTGCCACTCGATCTCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAGgtattt------tgaattcagtgacatgctttgttttggtccatacttcatg-actttttctctgcattggatag-------------------------
| | ||  | || || || ||||| ||||||||||  ||||| ||||||||||| || |||||||| || |||||  | ||||| || ||||| |||||||| | |      |    |   ||  || | || |     |   |  |||||  | ||| ||  |   ||   |                           
GGCCGCGTTGAGGGATGCCTACAAGAACAAGAAGTACTTGCCTCTCGATCTCCGCCCTAAGAAGACCAGGGCCATTCGCAGGAGGCTTACTAAGCACCAGgtttatatgtgctacccttcttgttattccttttaaatatatgtttttcattcattttatcattattttcattgctgttattcctctttattttagtgta

upper sequence: AT3G55170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0317g00130.t01 (Vitis vinifera), 5'ss of exon 3
GTCTGCTCTTAGAGAAGCATACAAAAACAAGAAGTTGTTGCCACTCGATCTCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAGgtatt--ttgaattcagtgacatgctttgttttggtccatacttcatgactttttctctgcattggatag-------------------------------
| ||||||| || ||||| ||||| ||||||||||  |||||||| ||||| || ||||||||||| ||||||||  | | | ||||||| || || |||||| |  ||   ||   |   ||||| | | ||| |   |  ||  | |  |||||        || |                                 
GGCTGCTCTGAGGGAAGCCTACAAGAACAAGAAGTACTTGCCACTTGATCTGCGCCCCAAGAAGACCAGAGCCATTCGCAAGCGACTCACCAAGCATCAGgtaatccttctttttgatatgatgctct-tgttgatttgttgtttctaatattttccggttgaaggttcatttttgtgaatatcaatttaatctttctttt
















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|86081163|gb|DR376920.1|DR376920
EST:     TCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAG                         GCGTCGCTGAAGACAGAACGAGAGAAGAAGAAAGACATGTACTTTCCAATT
genomic: TCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAGgtattttgaa ... cattggatagGCGTCGCTGAAGACAGAACGAGAGAAGAAGAAAGACATGTACTTTCCAATT
EST: gi|125219873|gb|EL233958.1|EL233958
EST:     TCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAG                         GCGTCGCTGAAGACAGAACGAGAGAAGAAGAAAGACATGTA
genomic: TCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAGgtattttgaa ... cattggatagGCGTCGCTGAAGACAGAACGAGAGAAGAAGAAAGACATGTA
EST: gi|222358188|gb|GH717948.1|GH717948
EST:     TCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAG                         GCGTCGCTGAAGACAGAACGAGAGAAGAAGAAAGACATGTACTTTCCAATT
genomic: TCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAGgtattttgaa ... cattggatagGCGTCGCTGAAGACAGAACGAGAGAAGAAGAAAGACATGTACTTTCCAATT
EST: gi|19741057|gb|AU226410.1|AU226410
EST:     TCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAG                         GCGTCGCTGAAGACAGAACGAGAGAAGAAGAAAGACATGTACTTTCCAATT
genomic: TCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAGgtattttgaa ... cattggatagGCGTCGCTGAAGACAGAACGAGAGAAGAAGAAAGACATGTACTTTCCAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGCTCTTAGAGAAGCATACAAAAACAAGAAGTTGTTGCCACTCGATCTCCGTCCCAAGAAGACTAGAGCCATCAGAAGGAGACTCACTAAACACCAGgtattttgaattcagtgacatgctttgttttggtccatacttcatgactttttctctgcattggatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA