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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATTTGCCACCTATACAAATGCAAAACGGATAGTGAAGCTGGTGAATGATGTTGGTGATGTTGTTAACAGCGATCCAGAGGTCAACGAATACCTAAAGgtaacttagaggtggctaagcgtgatgcttgctcacctgagattgtttttgatcagaaactgtcaatattacacatgtatgcatctctcaagatgaacta...

Basic information

species Arabidopsis thaliana
transcript AT3G46970.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G46970.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA08G45210.1 (Glycine max), 5'ss of exon 13
AGCATTTGCCACCTATACAAATGCAAAACGGATAGTGAAGCTGGTGAATGATGTTGGTGATGTTGTTAACAGCGATCCAGAGGTCAACGAATACCTAAAGgtaacttagaggtggctaagcgtgatgcttgctcacctgagattgtttttgat-cagaaactgtca--atattacac-atgtatgcatctctcaagatgaacta
 |||||||| || || |||||||| | | ||||||| | | ||||||||||||| |||| |||||| ||||| ||||| ||||||||||  ||| | |||||||||||    ||   ||      | || | | |  |    |||||||  |   |||||  |  |  ||| ||    || | | | | | | |  ||  ||| 
GGCATTTGCAACATACACAAATGCTATAAGGATAGTCAGGTTGGTGAATGATGTCGGTGCTGTTGTCAACAGTGATCCTGAGGTCAACGGCTACTTGAAGgtaacttaattttgtacaact----tcctagataaagtccttttgttttgaaaatagaaaaagataggatactaagtgatttttccctatattatcatatactt

upper sequence: AT3G46970.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 5'ss of exon 12
AGCATTTGCCACCTATACAAATGCAAAACGGATAGTGAAGCTGGTGAATGATGTTGGTGATGTTGTTAACAGCGATCCAGAGGTCAACGAATACCTAAAGgtaacttagaggtggctaagcgtgatgcttgctcacc-tgagattgttt--ttgatcagaaactgtcaatattacacatgtatgcatctctcaagatgaacta
|||||| || || || || ||||| ||| ||||||| |||||||||||||||||||||| |||||| ||||  ||||| || ||||| || ||  | |||||||  ||    |   |||   |   | | |  ||   | |  ||||||  | |  |       | ||  ||||||  || |   || ||| | ||  || | 
AGCATTCGCTACATACACCAATGCTAAAAGGATAGTCAAGCTGGTGAATGATGTTGGTGCTGTTGTCAACACTGATCCTGAAGTCAATGAGTATTTGAAGgtaaaatatctttaattaactttccagatggtgcaatataattttgtttgctcgcacttgtgtggccacaattacagttgaa---atgtctaatgagtaagtt
















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|86060247|gb|DR356004.1|DR356004
EST:     ATGTTGGTGATGTTGTTAACAGCGATCCAGAGGTCAACGAATACCTAAAG                         GTGGTATTTGTTCCAAACTACAATGTCACTGTAGCGGAGATGCTAATACCC
genomic: ATGTTGGTGATGTTGTTAACAGCGATCCAGAGGTCAACGAATACCTAAAGgtaacttaga ... gcttctccagGTGGTATTTGTTCCAAACTACAATGTCACTGTAGCGGAGATGCTAATACCC
EST: gi|124900392|gb|EH975010.1|EH975010
EST:     AACAGCGATCCAGAGGTCAACGAATACCTAAAG                         GTGGTATTTGTTCCAAACTACAATGTCACTGTAGCGGAGATGCTAATACCC
genomic: AACAGCGATCCAGAGGTCAACGAATACCTAAAGgtaacttaga ... gcttctccagGTGGTATTTGTTCCAAACTACAATGTCACTGTAGCGGAGATGCTAATACCC
EST: gi|124759742|gb|EH849872.1|EH849872
EST:     ATGTTGGTGATGTTGTTAACAGCGATCCAGAGGTCAACGAATACCTAAAG                         GTGGTATTTGTTCCAAACTACAATGTCAC
genomic: ATGTTGGTGATGTTGTTAACAGCGATCCAGAGGTCAACGAATACCTAAAGgtaacttaga ... gcttctccagGTGGTATTTGTTCCAAACTACAATGTCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCATTTGCCACCTATACAAATGCAAAACGGATAGTGAAGCTGGTGAATGATGTTGGTGATGTTGTTAACAGCGATCCAGAGGTCAACGAATACCTAAAGgtaacttagaggtggctaagcgtgatgcttgctcacctgagattgtttttgatcagaaactgtcaatattacacatgtatgcatctctcaagatgaacta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagatgaa