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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatttgtgaactaggtcttgaaaatagctgatcgataagtttactgttttccttggagatggtcagaagttattataaataggatattaaggaatata...

Basic information

species Arabidopsis thaliana
transcript AT4G00630.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 5'ss of exon 12
TTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaa--tttgtgaactaggtcttgaaaatagctgatcgataagtttactgttttccttggagatggtcagaa-gttattataaataggatattaaggaatata-
||||||||||||| | || ||||| || ||||| ||||| || ||||| || ||||| ||||| ||||||||||||||||| || || ||||| ||||||||||    | ||||     || | |   |   || || ||    | | ||   |  | |||| | |    || |||  |||  |||  |||  || | | ||| 
TTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTGGTCTTCTGTTAGGTCTTTTCTTTATGACGgtaaggactctgaatataatcatcattttttttg-tctatg---tcaatgagctgataggagtttgcttcaatgtttatatggataatataacaatgtacatat

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G058948_T01 (Zea mays), 5'ss of exon 11
TTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatt--tgtgaactaggt--cttgaaaatagctgatc---gataagtt--tactgttttccttggagatggtcagaagttattataaata----ggatattaaggaatata---------------------------------------------------------------------------------------
||||||||||||  |||| ||||| || || || ||||| || ||||| |||||||| ||||| || |||||||||||||| ||||| ||||| |||||||| | |   || ||     |  | | ||| |   | | |   |||| | |  || || | |  || ||| || ||  || ||  ||  |  |    ||  || ||  ||  ||                                                                                       
TTTGGCTGGTCTGTTACTAGCAGAAACAGAGTTCTCCTTACAGGTTGAGTCAGATATAGCTCCTTATCGTGGTCTTCTGTTAGGACTTTTCTTTATGACGgtgagtaccgtaaatataattgcattaaatttcttaaacactgatatgctgctagtgctatgtttcgag-tgttcctaactttgtaccatcatcatgggcatcaaacaaattaagttatcacagaccttgctactctaatagttactacatttaacttcatattaaacataattaaccattttttggctgggaactgaag

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G093643_T01 (Zea mays), 5'ss of exon 12
TTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatt--tgtgaactaggtcttgaaaatagctgat-cgataagtttactgttttccttggagatggtcagaagttattataaataggatattaaggaatata
||| ||||||||  |||| ||||| || || || || ||||| ||||| |||||||| ||||| || |||||||||||||| ||||| ||||| |||||||| | |  ||||||     |      || |  |  | |  |||   |  | |  | ||        ||   ||||  ||   ||    |||  |   |  || 
TTTAGCTGGTCTGTTACTAGCAGAAACAGAGTTCTCATTGCAGGTTGAGTCAGATATAGCTCCCTATCGTGGTCTTCTGTTAGGACTTTTCTTTATGACGgtgagtactgtgaatataattgcattaagaattatttctttaacactgatatactgctaatgttatgtttcaagt-gttcctaaccttataccatc-atcat-

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA18G46420.1 (Glycine max), 5'ss of exon 19
TTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatttgtgaactaggtcttgaaaatagctgatcgataagtt-tactgttttccttggagatg-gtcagaagt---tattataaataggatattaaggaatata-
 ||||||||| ||||||| ||||| |||||||||||||| || |||||||| ||||| |||||||| ||||| ||||| ||||| |||||||| |||||||||  |   |||     | |  ||| |  |  ||| || | || || ||||||  |||   ||| | || |  |   |||| ||||| |    |   |   | |  
-TTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTGGCCTTCTTTTGGGGCTCTTCTTTATGACGGtaggtgccgaa-----tatcaaaattcacaaatctattaattgtattgttttatttgttcatgtgacaaatatttttattttaaattgcggttatggttgtgttg

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA09G39770.1 (Glycine max), 5'ss of exon 15
TTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatttgtgaactaggtcttgaaaatagctgatcgataagtt-tactgttttccttg---gagatggtcagaagttattataaata-ggatattaaggaatata
|||||||||| ||||||| ||||| |||||||||||||| || |||||||| ||||| ||||| || ||||| ||||| ||||| |||||||| |||||||||  |  ||||     | |  ||| |  |  ||  || | || || ||||||  |||   | ||   |      | |||     || || | |   |  || | 
TTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTGGCCTTCTTTTGGGGCTCTTCTTTATGACGgtaggtgctgaa-----tatcaaaattcacaaatttattaattgtattgttttatttgtttgtgacatttttttttaattgcggttatggttgtgttgctatttc

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 5'ss of exon 10
TTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatttgtgaactaggtc---ttgaaaatagctgatcgataagtttactgttttccttggagatggtcagaagttattataaataggatattaaggaatata
|||||||||| | || |||||||| |||||||||||||| || |||||||||||||| |||||||| ||||| ||| | ||||| ||||||||||||||||||  || |  || | | |   |  || | ||    |   | |    |   |      |  |  | ||    | |  ||  || |    | ||  |  | |  
TTTGGCTGGTTTGCTTCTTGCAGAAACTGAATTTTCCTTACAGGTTGAATCAGATATTGCTCCATATCGTGGCCTTTTATTGGGTCTCTTCTTCATGACGgtaggttcttcaccatgccatttccaagagaggcatttatttatccaatcctaacatataaacctcgtttctattccttg-aagttacctgtttggagaga--

upper sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ07595 (Selaginella moellendorffii), 5'ss of exon 9
TTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatttgtgaactaggtcttgaaaatagctgatcgataagtttactgttttccttggagatggtcagaagttattataaataggatattaaggaatata
| | ||||| || ||  |  |||| || || ||  |  ||||||||||||| ||||| || ||||| || ||||||||  ||||||| ||||| ||||| |||| | ||   ||      | |||| |  |        || | | | | |  | |  | |    |||                                
TCTTGCTGGACTCCTTTTGTCAGAAACCGAGTTCGCTCTGCAAGTTGAATCCGATATTGCACCATATCGGGGTCTTCTTCTGGGACTTTTCTTTATGACAgtaagtggtttcct-----ctaaaaacaa-tatcttccgagctcattatctggcgta-acacctgcag--------------------------------

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|86068174|gb|DR363931.1|DR363931
EST:     CAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACG                         GTGGGCATGTCCATTGATCCAAAACTTCTTCTCGCCAACTTCCCTCTCATA
genomic: CAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatttgtg ... ataaaatcagGTGGGCATGTCCATTGATCCAAAACTTCTTCTCGCCAACTTCCCTCTCATA
EST: gi|86068176|gb|DR363933.1|DR363933
EST:     CAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACG                         GTGGGCATGTCCATTGATCCAAAACTTCTTCTCGCCAACTTCCCTCTCATA
genomic: CAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatttgtg ... ataaaatcagGTGGGCATGTCCATTGATCCAAAACTTCTTCTCGCCAACTTCCCTCTCATA
EST: gi|86068175|gb|DR363932.1|DR363932
EST:     CAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACG                         GTGGGCATGTCCATTGATCCAAAACTTCTTCTCGCCAACTTCCCTCTCATA
genomic: CAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatttgtg ... ataaaatcagGTGGGCATGTCCATTGATCCAAAACTTCTTCTCGCCAACTTCCCTCTCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTGGTCTTCTGTTGGGACTCTTCTTCATGACGgtaatttgtgaactaggtcttgaaaatagctgatcgataagtttactgttttccttggagatggtcagaagttattataaataggatattaaggaatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaata