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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAGAAAGAGGGTTTACTGCAATTGGGACTGGTGGCAATGACTTTGTGCATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttcgtcctcttaaaagtatctagatgatttaccggcttatactatctttttttgatacgatatttgctagtgtcttctatacaatattttggc...

Basic information

species Arabidopsis thaliana
transcript AT1G27385.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G27385.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G025042_T01 (Zea mays), 5'ss of exon 3
AACAGAAAGAGGGTTTACTGCAATTGGGACTGGTGGCAATGACTTTGTGCATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttcgtc-ctcttaaaagtatctagatgatttaccggcttatactatctttttttgatacgatatttgctagtgtcttctata----caatattttggc
 ||||| ||||| ||||| |||||||| ||||| ||  |||| ||||| ||  | ||||| |||||||||||||||||| || |   |  ||||||  |||| |  |||  ||  ||||| || ||| |  |     |    | |   |  |      | ||||  ||    ||||||||  ||         ||||| ||  | 
CACAGATAGAGGATTTACAGCAATTGGCACTGGAGGTGATGATTTTGTCCAGTCAATGGTAGTTGCTGTTGAATCTGTTCTTCAAGAATCAATTCCCAAGgttagtttttatcattcttataattatttgtaaaccatgt-agttatcaacaagaagatgtgattagac---tgctagtgctttgcgcggagccaatacttccg-

upper sequence: AT1G27385.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv01s0010g03660.t01 (Vitis vinifera), 5'ss of exon 3
AACAGAAAGAGGGTTTACTGCAATTGGGACTGGTGGCAATGACTTTGTGCATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgta-atatttcgtcctcttaaaagtatctagatgatttaccggcttatactatctttttttgatacgatatttgctagtgtcttctatacaatattttggc
|||||  |||||||||||||||||||| ||||| ||  | || |||||||| ||||||||||||||||||||||||||  || | |  | ||| || |||||| |||  ||      |  |||   | | | ||| | |   | ||      |  |   |||||||       |  |    |||  |    |   |||   
AACAGTTAGAGGGTTTACTGCAATTGGAACTGGAGGTGACGATTTTGTGCAAGCTATGGTTGTTGCTGTTGAATCTGTACTTCAACATCCAATACCTGAGgtacatagatcacttgttgcaaatgtttttgttgactaagatgttttctagtttatgcattgatacatccaaggaaataaactttaaggtgaccatttaa-
















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|86080659|gb|DR376416.1|DR376416
EST:     ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAG                         GACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
genomic: ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttc ... tccattttagGACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
EST: gi|301503145|gb|HO208685.1|HO208685
EST:     ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAG                         GACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
genomic: ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttc ... tccattttagGACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
EST: gi|19742694|gb|AU228047.1|AU228047
EST:     ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAG                         GTCTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
genomic: ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttc ... tccattttagGACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
EST: gi|19876202|gb|AU237033.1|AU237033
EST:     ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAG                         GTCTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
genomic: ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttc ... tccattttagGACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
EST: gi|86079028|gb|DR374785.1|DR374785
EST:     ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAG                         GACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
genomic: ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttc ... tccattttagGACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGTCGGTGAAT
EST: gi|125228187|gb|EL242272.1|EL242272
EST:     ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAG                         GACTGTGTAAAGCAGACTTTATCAAGCAAAGG
genomic: ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttc ... tccattttagGACTGTGTAAAGCAGACTTTATCAAGCAAAGG
EST: gi|19798774|gb|AU230064.1|AU230064
EST:     ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCCACAAATTCCAGAG                         GACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGTGGTCGGTGAA
genomic: ATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttc ... tccattttagGACTGTGTAAAGCAGACTTTATCAAGCAAAGGAAAATATGT-GTCGGTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAGAAAGAGGGTTTACTGCAATTGGGACTGGTGGCAATGACTTTGTGCATGCTATGGTTGTTGCTGTTGAATCTGTTATTGACCGACAAATTCCAGAGgtaatatttcgtcctcttaaaagtatctagatgatttaccggcttatactatctttttttgatacgatatttgctagtgtcttctatacaatattttggc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT