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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgcttgtatcttcctatttattaccagaaattgcgctctatcacagcaagagatggaattcttgaagaaacttcatttttggtaaccttaatcta...

Basic information

species Arabidopsis thaliana
transcript AT3G11910.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11910.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 15
CACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgcttgtatcttcctatttattaccagaaattgcgctctatcacagcaagagatggaattcttgaagaaacttcatttt-tggtaaccttaatcta
  | ||||||||||||||  ||||||||||||||||||| ||| |||| ||  |    ||  ||||    |  |||||     |  |  | ||    ||||||  |  |||      |  |||| | | |    ||    |   ||      |    ||| |  |     |   ||   ||| | | | |    | ||   
TGCAGAGCAAATTGGAAAACATATATATTTTGATCTTGTGGATTATGACAACATCCAAAGCCTTCGGGCACCTAAACATTTGACAATAAACCAGGCCAAGgtaactttttgctgagcctcatttgtcatccatgatatatcaaaatgtgtatatctaatgaatatacgatatgcacagaattgtattgcattgatgatgc-

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 11
CACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgta---catgcttgtatcttcctatttattacca--gaaattgcgctctatcacagcaagagatggaattcttgaagaaacttcatttttggt--aaccttaatcta----------------
 |  ||||||||||| ||| ||||||||||||| || || || |||||||||||  | || || ||||| ||||| |||   |  |||      || ||||||     |||    |  ||| |  ||  || ||  | |||       |    |   | |||     || |||    ||| |  | |  |  |  ||| |   |  |                
GAAGGAGCAAATTGGCAAGGATATATATTTTGACCTGGTGGACCATGAAAAAGTTCGTAGCTTCCGAATTCAGAAGCAGTTACTGTTTACCACTTTCAAGgtaaggtgtgcaaacaagttcttggttcgtagcattggaatgctaaatttctgctatacgagtacacatgcttctgtaaaatcaactggtaatttaacttctgttgaataaattgtttaatag

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 15
CACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgcttgtatcttcctatttattaccagaaattgcgctctatcacagcaa-gagatggaattcttgaagaaacttcatttttggtaaccttaatcta
 |  || || ||||| |||||||||||||||||||| || || |||||||| ||  | || || || || ||||| ||    || |||     ||||||||||     |  ||    |||| || ||   |  ||     | || | |       | |||  |   ||  ||   | || |   ||    ||    | || 
GAAGGAACAGATTGGTAAGAATATATATTTTGATCTGGTGGACCATGAAAAGGTTCGCAGCTTCCGCATACAGAAGCAACTACCTTTTACTTCATTTAAGgtaaccattcctaaacacctagtttttcataacaaggatacgctgttaagtttctgtgatataggcctataacttattttagggttttgcactgctacct-

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 5
CACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgcttgtatcttcctatttattaccagaaattgcg-ctctatcacagcaagagatggaattcttgaagaaacttcatttttggtaaccttaatcta
 |  |||||||| || |||||||||||||||||||| || || |||||||||||    ||||| || || ||||| |||   || |||     ||| ||||||   ||    |    ||||  | ||     |||    | ||  ||       |    |||| | ||  |     |||  |    | |     |  |  |
AAAGGAGCAAATCGGTAAGAATATATATTTTGATCTGGTGGACCATGAAAAAGTTCACAGTTTCCGCATTCAGAAGCAGTTGCCTTTTACTTCATTCAAGgtattggcccaaaaaaccctacatgtttatttaaaccatggcttcatggttatgatttttgga-tactacagtcctctttgtaagagattgagctgctaca

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GRMZM2G014805_T01 (Zea mays), 5'ss of exon 15
CACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgcttgtatcttcctat---ttattaccagaaattgcgctctatcacagcaagagatggaatt---cttgaagaaact--tcatttttggtaaccttaatcta
 |  ||||||||||| || |||||||||||||| || || || |||||||||||  | || || || || ||||| |||   || |||     |||  |||||   ||    |    ||||    || ||||     |||  | | | |     | | ||    | ||   |  ||   | ||  |||||| ||||            
AAAGGAGCAAATTGGTAAAAATATATATTTTGACCTGGTGGACCATGAAAAAGTTTGCAGCTTCCGCATTCAGAAGCAGTTGCCTTTTACTGCATTCCAGgtaatggcccaaaaaaccctacatgtttttacttagcattatggtttttggatactacaggcctatttgcacgggattgagctgctcatttatggttgtt--------

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 15
CACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtaca---tgcttgtatctt----cctatttattaccagaaattgcgctctatcacagcaagagatggaa--ttcttgaa--gaaacttcattt-ttggtaaccttaatcta
  | ||||||||||||||| ||||||||||||||||||| |||||||| |||||  | |||||||| || |||||||||   || |||   |  || |||||| |   | |||   | ||    |  || |  ||     || |  | |||||       |    ||  |  ||||| ||  ||| ||||   |  ||||            
TGCAGAGCAAATTGGAAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTCCGCAGTTTTCGCATTCAGAAACAGTGGCCTTTTACCCTTTTCAAGgtatagtttacttcggttttgtctctgatatgataaagttaaatttgttctattgttatcatcattgccagtttctttaattgaagcttcgggtactggt------------

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|125261735|gb|EL275820.1|EL275820
EST:     GAGTTTTCGTAATCCAGAAACAGACCCCCTTTCAACAATTTAAG                         GAAGAGGTAGCCAAAGAGTTTGGTGTCCCGGTTCAACTACAGCGGTTCTGG
genomic: GAGTTTTCG-AATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgctt ... cctcatgtagGAAGAGGTAGCCAAAGAGTTTGGTGTCCCGGTTCAACTACAGCGGTTCTGG
EST: gi|124919850|gb|EH993588.1|EH993588
EST:     AAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAG                         GAAGAGGTAGCCAAAGAGTTTGGTGTCCC
genomic: AAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgctt ... cctcatgtagGAAGAGGTAGCCAAAGAGTTTGGTGTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGACCCCCTTTCAACAATTTAAGgtacatgcttgtatcttcctatttattaccagaaattgcgctctatcacagcaagagatggaattcttgaagaaacttcatttttggtaaccttaatcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcgctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaa