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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagcagagactaattctcttttaagtgagatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag

Basic information

species Arabidopsis thaliana
transcript AT1G70730.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 10
------GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgta-------gcagagactaattctcttttaagtgagatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag
      | |||||  |  | ||| |     ||||||      | || ||||| ||||| || || |||||||||||||| || || |||||||| || |||||||||||       ||  |||    ||    |||  ||     | || |  ||    | | |  |     | |  || ||  |    |                 
TTGACCGGATGGGCCTTGGAAAATCCTCAAATGCTG------AACCCCCAGAATTTGGTGCTGCAGCTGATGGTGATGCTGATCGCAACATGATTCTGGGTAAAAGgtattcttcagcctagatagcttgaagtttttgtatatactcataagtgctatgagaaatttatgatgtgtcctttgccttctag----------------

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G109383_T02 (Zea mays), 5'ss of exon 10
---GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagca---------gagactaattctcttttaagtg------agatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag
   |||||||  |  |  ||| | ||  | |   ||  |||||||| || ||||| || || |||||||| ||||| ||||| |||||||| || |||||||||||  |         |   || ||| |||   || |       ||||   ||| | | | |  | ||  |  || |||||| ||  |     |||              
AACGCATGGGTCTTGG--AAAGTCATCCT-CAAATGTTGAGCCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTTGGTAAAAGgtatgatctgtttgagtatcttattttctacaaaatttgttacagattctagaaaagcgcaaggaattcatgacactcccctttgccttgctatag-------------

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 10
---GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgta-gcagagactaattctcttttaagtgagatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag---------
   | |||||  |  |  ||| | ||  | |   ||  || ||||| || ||||| || || |||||||| ||||| ||||| |||||||| || ||||||||||| |    |    | | |||| | |   |||      |  | ||    ||||     |    | |    ||   |  ||   ||  ||  || |         
AACGGATGGGTCTTGG--AAAGTCATCCT-CAAATGTTGAACCTCCTGAATTTGGTGCTGCAGCTGATGGAGATGCTGACCGCAACATGATTCTGGGTAAAAGgtatgatctgttcgagtatcttattatgtaga------aagtttgttttggattctagataagcacaaggaattcatgatgcttcccctttgccgtgtttatag

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 10
---GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagcagagactaattctcttttaagtgagatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag-
   | ||||||||| | ||| | ||     |    |  || || ||||||||||| || ||| |||||||||||||||| || |||||||| || ||||||||||||          ||  | || |  || | | |     || |  |     |  | |  | |    || |        |||| | | |  |    
CTCGTATGGGATTGGGCAAATCCGAAC---CACAAGATGATCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAGgtagtg--------ttgcccttaatttgtggtga-----atttaaatattctccaactttttgtgtgtaatatctgtgtatcccctgtttgttag

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA03G05150.1 (Glycine max), 5'ss of exon 3
---GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagcagagactaattctcttttaagtgagatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag-
   | ||||||||| | ||| ||||  |  |    |  ||||| ||||||||||| || ||| |||||||||||||||| || |||||| | || ||||||||||||          || || || |  || ||| |     || |  |     | || |  | |    || |        |||| ||| |  |    
CTCGTATGGGATTGGGCAAATCTGA--ACCCCAA-GATGAGCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGGTTCTTGGTAAAAGgtagtg--------ttgtccttaatttgtgatga-----atttaaatattctctaac-ttttttgtgtaatatctgtgtatcccttgtttgttag

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 10
---GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagcagagactaattctcttttaagtgagatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag-
   | ||||||||| | ||| | ||  |  |    |  ||||| ||||||||||| || ||| |||||||||||||||| || |||||| | || ||||||||||||          || || || |  || ||| |     || |  |     | || |  | |    || |        |||| | | |  |    
CTCGTATGGGATTGGGCAAATCCGA--ACCCCAA-GAAGAGCCCCCAGAGTTTGGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGGTTCTTGGTAAAAGgtagtg--------ttgtccttaatttgtgatga-----atttaaatattctctaac-ttttttgtgtaatatctgtgtatcccctgtttgttag

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 11
---GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagcagagactaattctcttttaagtgagatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag
   | ||||||||| ||||| | ||||   ||      ||||| ||||||||||| |||||| |||||||||||||||| || ||||||||||| || ||||||||| |  |   | |||  || |       ||       || ||       | |   |    |    ||| |    ||| ||            
CATGTATGGGATTGGGTAAATCAGATG---CTAAAAATGAGCCACCAGAGTTTGGTGCCGCTTCTGATGGTGATGCAGATCGTAACATGATCCTTGGCAAAAGgtagtactg--cacttcatttctggaaagaatacttattatttgacataagtcttaaatcacctgatttaccttgcaatgtcag----------

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S4_12V6.2 (Physcomitrella patens), 5'ss of exon 11
------GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagcagagactaattctcttttaagtgagatcacagagatgt-----ggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag-
        ||||||||| | || ||| |     |   || ||||  ||| || || || |||||||||||||||||||| ||||||||||||||  | || || | |||   ||       || | | || |     |       || |     | ||  ||| |              | | |      ||    | |  ||   
TGCAAGTTATGGGATTGGGCAAGACTCA----ACC--TGACGAGATTCCGGAATTCGGTGCCGCTGCTGATGGTGATGCTGACCGAAACATGATTTTGGGCAAGAAgtatgtgatcagggctcccatctacgactccttgtcttaatctatctggaagttgatgtgatttctgtattcctgatcccgctaattctgtgttagcttt

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|116415445|gb|EG458037.1|EG458037
EST:     GGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAG                         GTTTTTCGTAACTCCTTCGGATTCAGTTGCTATAATTGCTGCAAATGCTGT
genomic: GGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagcagaga ... ttctccgcagGTTTTTCGTAACTCCTTCGGATTCAGTTGCTATAATTGCTGCAAATGCTGT
EST: gi|125083212|gb|EL143869.1|EL143869
EST:     AAACAATGATCCTCGGTAAAAG                         GTTTTTCGTTAACTCCTTCGGATTCAGTTGCTATAATTGCTGCAAATGCTG
genomic: AAAC-ATGATCCTCGGTAAAAGgtagcagaga ... ttctccgcagGTTTTTCG-TAACTCCTTCGGATTCAGTTGCTATAATTGCTGCAAATGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGCCTCCAGAGTTTGGCGCCGCTGCTGATGGTGATGCAGACCGAAACATGATCCTCGGTAAAAGgtagcagagactaattctcttttaagtgagatcacagagatgtggagcggatataccactctccccgttaaccaaaaatatctcttctccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT