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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgctgagagagagagggagagagagattcatattcatttgccattttctcactctgggttttgtgtgga...

Basic information

species Arabidopsis thaliana
transcript AT3G08850.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 5'ss of exon 10
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttccc----ttttgctgagagagagagggagagagagattcatattcatttgccattttctcactctgggttttgtgtgga
 ||||| ||||| || |||||| ||||||| ||||| || |||||||||||||| |||||  | ||||| || || || ||| ||||||||||||||||||        ||| |  |   |  |   |    |  |  ||          |      |||    |  ||  |   | | | ||  | |   ||     |     
GAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTCAGgcaagacattttttccatccagctattcaagatgctagtgttttttttttgttatttgagtggtaagttggtaaccgactctccaaatgatggcaaaata----

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 9
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgctgagagagagagggagagagagattcat--attcatttgccattttctcactctgggttttgtgtgga-
 ||||| ||||| || |||||| ||||||| ||||| || |||||||||||||| |||||  | ||||| || || || ||| ||||||||||||||||||     |||  | | |    ||    |  ||      |  || |             ||  |  | |  |  |    |  || |||||     |  ||   | 
GAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTCAGgca---agacatttttttccatccagctattcaagatgctagtgttttttttttttgttatttgagtggtaagttggtaactgactctccaaatgatggcaaa

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G460090_T01 (Zea mays), 5'ss of exon 1
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgctgagagagagagggagagagagattcatattcatttgccattttctcactctgggttttgtgtgga-
|||||| |||||||| || |||||||| |||||||| ||||||||||||||||| |||||| | ||||| || || || |||||||| || |||||||||||       |||   ||   | || |      |   | |      |  | |   || || |  ||       | |   ||  ||||  | |   | |||  
AAGTCCTTTTTTTACGGAACAACTGACGGCTTTTGAAGTGTGGCTTGATCATGGCTCTGAGGACAAGAAACCTCCTGAACAGTTACCCATAGTTCTTCAGgtaaggcattttgcttatacacttacatacaagtcaatattatctgtaaaatccagtttaactttgtaacctcttcacctttctctaagctgc-tatggtt

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 10
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgctgagagagagagggagagagagattcatattca-tttgccattttctcactctgggttttgtgtgga-------
||||||||||||||| || |||||||| ||||| || ||||||||||||||||| || ||| | ||||| || || || |||||||| || |||||||||||    ||| || |     |  |||| |  || |    |     |      |  | | |||  || | |||   |  || |  | ||    ||| |    |       
AAGTCCGTTTTTTACGGAACAACTGACGGCTTTCGAAGTGTGGCTTGATCATGGCTCCGAGGACAAGAAACCTCCTGAACAGTTACCCATAGTTCTTCAGgta---agactttt-----tgctttcacacttacattcaagtcaattatttgtaaaactcactttaactttataaccttattgcccttcacttttttgctatagtttt

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA18G44210.1 (Glycine max), 5'ss of exon 10
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgctgagagagagagggagagagagattcatattcatttgccattttctcactctgggttttgtgtgga-----
 ||| | ||||| || |||||  ||||||| |||||||| |||||||| ||||| ||||| |||||||| ||||| |||||||| ||||| |||||||||||||   |||   |||  |  | ||   |     |           |  |    | | | |   |  || |    |   | ||  ||  |||| ||         
TAGTACATTTTTCACCGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAGCAGTTGCCTATAGTTCTTCAGgtgc---gatccttgtcttggtctttgttaccatttgagccattttgttggctcataat-actcttgttaggtggtaggttaca-tgatttttatgaaatcagct

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 10
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgct-gagagagagagggagagagagattcatattcatttgccattttctcactctgggttttgtgtgga--
 ||| | ||||| ||||||||  ||||||| |||||||| |||||||| ||||| ||||| |||||||| ||||| || ||||| ||||| |||||||||||||   |||   |||  |  ||||         | |||  |    |   |      ||||   ||   |||    ||||    | |  ||    |  |    
TAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTCAGgtgc---gatccttgtcttggtttttgtaaccatttgagccattatgttggctcataattctcgttaggttgtaggtttcgtgatttttgtgaaatcagctgt

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 5'ss of exon 10
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgctgagagagagagggagagagagattcatattcatttgccattttctcactctgggttttgtgtgga---------
|||||| || || |||||||| ||||| ||||||||||| ||||| ||||||||||| || || ||||| ||||| |||||||| || ||||||||||||||       ||||  |  ||  | |   ||          ||    | ||   |   ||  | ||  |   || || | | |   ||| ||||  ||  |         
AAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTCAGgtaggatattttccttgattcctataaattcc--------aggactgtagtttggtctttgt-tttttccccccttatattatggtggtttttaagtatatttttatgg

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 5'ss of exon 10
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgctgagagagagagggagagagagattcatattcatttgccattttctcactctgggttttg-tgtgga----
 ||||| ||||| || |||||| |||||||||| ||||||||||| || ||||| |||||    ||||||||||| |||||  | ||||| |||||||| ||   |||  |  |  |   || |    |  |||| |||  |    | |   |  ||| |||  ||||     |  |  | |     | || || |||       
TAGTCCTTTTTTCACAGAGCAATTGACAGCTTTCGAGGTGTGGCTGGAGCATGGTTCTGAAAGGAAGAAGCCACCTGAGCAACTTCCTATCGTTCTTCAAgta--tagtgtgatcaagccatctaag-tagtgctcagactgga--gtatctatggatgcatgctcatgaaaaacgtagttagcgacgtttctgatgttctgtat

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 5'ss of exon 10
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgctgagagagagagggagagagagattcatattcatttgccattttctcactctgggttttgtgtgga---
 ||||| ||||| || |||||| ||||||| ||||| |||||| | || ||||| |||||||  ||||||||||| |||||| | ||||| ||||| |||||   |||  |  |||| | | | | ||  |   |   |   |||   ||  |   ||  |      |||   |   | |   |   |   |||  |      
TAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGCAGgta--tagtgtgatgtagt-actgtgccaataagtagtactcagattcaggtacctatgtaggagttttttggagggtttagtttgcgtcgttgactatgttc

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|116411083|gb|EG453675.1|EG453675
EST:     ATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAG                         GTGTTACTTAGCCAGTGCCATCGGTTTCGTGCTCTTGTACTTCTTGGAAGA
genomic: ATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagat ... tttgtttcagGTGTTACTTAGCCAGTGCCATCGGTTTCGTGCTCTTGTACTTCTTGGAAGA
EST: gi|116411080|gb|EG453672.1|EG453672
EST:     ATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAC                         GTGTTACTTAGCCAGTGCCATCGGTTTCGTGCTCTTGTACTTCTTGGA-GA
genomic: ATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagat ... tttgtttcagGTGTTACTTAGCCAGTGCCATCGGTTTCGTGCTCTTGTACTTCTTGGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGATCATGGATCTGAGCATAAGAAGCCACCGGAGCAGTTACCTATTGTTCTTCAGgtgcctagatttctgtacttattttcccttttgctgagagagagagggagagagagattcatattcatttgccattttctcactctgggttttgtgtgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcactct