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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaagatcaacttcgctttcttctttacctcgttttgtcttttttgcatctttgtgtctgtctgtgtttttattcccccagtagagtagattttt...

Basic information

species Arabidopsis thaliana
transcript AT1G75060.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os10g21460.1 (Oryza sativa), 5'ss of exon 2
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaagatcaacttcgctttcttctttacctcgttttgtcttttttgcatctttgt---gtctgtctgtgtttttattcccccagtagagtagattttt
||| || || || || || |||||||| ||||| || || ||||| || || || |||||||| ||||| |||||||| ||||| || |||||||||||||| |     | ||  |  | ||  |    || | |   |||   |||     |||||  |    | ||      | |  |||  |    | || |   |||||
CAAGGTGGTGGTCACCGGCAACAACCGCACCAAGTCGGTGCTCGTTGGCCTCCATGGCGTCGTCAAGAAGGCCGTCGGGCTCGGGGGATGGCATTGGCTGgtaatttc-gctctgccccactcgcaa--ttgctttaatttcgatttcgcagatcttgatttgatttgatacaatgtgaatttgctttttcgattgttttttt

upper sequence: AT1G75060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA04G03620.1 (Glycine max), 5'ss of exon 1
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaagatcaacttcgct-ttcttctttacctcgttttgtcttttttgcatctttgtgtctgtctgtgtttttattcccccagtagagtagattttt
|||||||||||| || ||||| ||||| |||||||| || ||||| ||||||||||| ||||||||||||||||| ||||| || || |||||||||||||| |       |  | ||  ||   |||||  ||  |  |  |  || |     |||| ||  |  | | || |||       |   ||     | |||| 
CAAAGTTGTCGTAACCGGAAATAACCGCACCAAATCGGTGCTCGTTGGTCTTCAAGGTGTCGTTAAGAAAGCCGTTGGACTAGGCGGATGGCATTGGCTGgtaattttcattttatttatctacccttctaaacgacactgcggattatcaatttcttcgttccaatttttggtttctaatgtcgtctatttccgttttt-

upper sequence: AT1G75060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA04G03630.1 (Glycine max), 5'ss of exon 1
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaagatcaacttcgct-ttcttctttacctcgttttgtcttttttgcatctttgtgtctgtctgtgtttttattcccccagtagagtagattttt
|||||||||||| || ||||| ||||| |||||||| || ||||| ||||||||||| ||||||||||||||||| ||||| || || |||||||||||||| |       |  | ||| ||   |||||  ||  |  |  |  || |     |||| ||  |  | | || ||   |     |       |  ||||||
CAAAGTTGTCGTAACCGGAAATAACCGCACCAAATCGGTGCTCGTTGGTCTTCAAGGTGTCGTTAAGAAAGCCGTTGGACTAGGCGGATGGCATTGGCTGgtaattttcattttatttctctacccttctaaacgacactgcggattatcaatttcttcgttccaatttttggttgc-taatgtcgtctatttccattttt

upper sequence: AT1G75060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA06G03710.1 (Glycine max), 5'ss of exon 1
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaagatcaacttcgctttc-ttctttacctcgttttgtctttt---ttgcatctttgtgtctgtctgtgtttttat-tcccccagtagagtagattttt
|||||| ||||| || ||||| ||||| |||||||| || ||||||||||||||||| || |||||||| ||||| ||||| ||||| |||||||||||||| ||      |  | ||| ||  | ||| | |   |  || || || |   |||| |  || |   | |  ||   || || ||    | | |  |   |||  
CAAAGTGGTCGTAACAGGAAATAACCGCACCAAATCGGTGCTCGTCGGTCTTCAAGGTGTTGTTAAGAAGGCCGTTGGACTAGGTGGATGGCATTGGCTGgtaagt-----tttatttctctaccattcataatgacaattcgtattatgaattgcttgattctaattttgggttgcttaatgtcgtttatttgcattattttac

upper sequence: AT1G75060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA06G03720.1 (Glycine max), 5'ss of exon 1
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaagatcaacttcgct-ttcttctttacctcgttttgtcttttttgcatctttgtgtctgtctgtgtttttattcccccagtagagtagattttt----
|||||| ||||| || ||||| ||||| |||||||| || ||||| ||||||||||| || |||||||||||||| ||||| ||||| |||||||||||||| ||      || | ||| ||  ||||| | |   |  || || || |    | |||  |     | |  | ||   |     || |    |  ||| ||    
CAAAGTGGTCGTAACAGGAAATAACCGCACCAAATCGGTGCTCGTTGGTCTTCAAGGTGTTGTTAAGAAAGCCGTTGGACTAGGTGGATGGCATTGGCTGgtaagt-----tctatttctctactcttcataatgacaattcgtattatgaatagcttgattctaattttgggttgcttaatttcatttatttgcattattgtgg

upper sequence: AT1G75060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv18s0001g11970.t01 (Vitis vinifera), 5'ss of exon 1
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgag-caaagatcaacttcgctttcttctttacctcgttttgtcttttttgcatct---ttgtgtctgtctgtgtttttattcccccagtagagtagattttt
||| || ||||| || || || ||||||||||||||||| || || || || || ||||| || ||||| || ||||| || |||||||||||||||||||| |  |       ||    ||||   | |       |  || |    ||||  | |   |||||  |   || | || || |       |    | ||     
CAAGGTAGTCGTCACCGGCAATAACCGTACCAAATCTGTGCTTGTGGGCCTCCAGGGCGTGGTCAAGAAGGCTGTCGGCCTTGGTGGTTGGCATTGGCTGgtaattcttttgataatcgtgcttctatttgagaaaagggtttttgggtttgtgtttgtcttgtggttaattgggattataatgtggttcttattttgaa----

upper sequence: AT1G75060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S83_77V6.1 (Physcomitrella patens), 5'ss of exon 2
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaa--gatcaacttc-gctttcttctttacctcgttttgtcttttttgcatctttgtg-tctgtctgtgtttttattcccccagtagagtagattttt---------------------------------
 |||||  | ||||| |||||||| || |||||||||||| | || |||||||| |||||||| | |||||| || || || ||||| |||||||||||||| | ||    ||  |||||  |    |||  |     |  |||||  | ||   || ||   | | | |||       | | | |  | |       |  ||                                  
GAAAGTGCTGGTTACAGGAAACAATCGCACCAAATCTGTTTTGGTTGGTCTTCACGGCGTCGTCACGAAAGCTGTGGGTCTGGGTGGCTGGCATTGGCTGgtaatcattttgaagaacttgaggcagctttctggtgcctatttgtaatgttaatattttcacggtgtatcttctgccatttactcttaattcctcgaaagttcatcgaagtcaccaattttgtgttcacgtggcag

upper sequence: AT1G75060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ17425 (Selaginella moellendorffii), 5'ss of exon 1
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaagatcaacttcgctttcttctttacctcgttttgtcttttttgcatctttgtgtctgtctgtgtttttattcccccagtagagtagattttt----
||| ||  | || |||||||||||||| || ||||| || |||||||| || || ||| |||| ||||| ||||| ||||| || || |||||||||||||| |||||| |  | |   ||||||    || | | |  ||  || |   |  |  |||     | | |  |||  | | ||    |        || ||    
CAAGGTCATTGTGACTGGAAACAACCGCACGAAATCCGTGCTCGTCGGGCTACACGGCATCGTGAAGAAGGCCGTGGGACTTGGCGGCTGGCATTGGCTGgtaagcaaaaaaaatcaatgctttc---cttgctttgcatt-cctctccggtttgattgatcacggcggcttttcaaattccatcttgcttcttcttcttggaa

upper sequence: AT1G75060.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ35053 (Selaginella moellendorffii), 5'ss of exon 1
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaagatcaacttcgctttcttctttacctcgttttgtcttttttgcatctttgtgtctgtctgtgtttttattcccccagtagagtagattttt----
||| ||  | || |||||||||||||| || ||||| || |||||||| || || ||| |||| ||||| ||||| ||||| || || |||||||||||||| ||||||   ||| | |  |   ||| || | | |  ||  || |   |  |  |||     | | |  |||  | | ||    |        || ||    
CAAGGTCATTGTGACTGGAAACAACCGCACGAAATCCGTGCTCGTCGGGCTACACGGCATCGTGAAGAAGGCCGTGGGACTTGGCGGCTGGCATTGGCTGgtaagcaaaa--caaat-caatgctttccttgctttgcatt-cctctccggtttgattgatcacggcggcttttcaaattccatcttgcttcttcttcttggaa

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|116401944|gb|EG444536.1|EG444536
EST:     TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTG                         GTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
genomic: TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaag ... aaattttcagGTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
EST: gi|116401945|gb|EG444537.1|EG444537
EST:     TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTG                         GTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
genomic: TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaag ... aaattttcagGTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
EST: gi|116401953|gb|EG444545.1|EG444545
EST:     TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTG                         GTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
genomic: TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaag ... aaattttcagGTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
EST: gi|86076785|gb|DR372542.1|DR372542
EST:     TTCAAGGCGTCGTTAAAAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTG                         GTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
genomic: TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaag ... aaattttcagGTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
EST: gi|116401954|gb|EG444546.1|EG444546
EST:     TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTG                         GTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
genomic: TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaag ... aaattttcagGTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
EST: gi|116401956|gb|EG444548.1|EG444548
EST:     TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTG                         GTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT
genomic: TTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaag ... aaattttcagGTTTTGACTAATGGAATTGAAGTGAAGTTGCAGAGGAATGCGCTTAGTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGTTGTCGTTACTGGAAACAACCGTACCAAATCTGTTCTCGTCGGTCTTCAAGGCGTCGTTAAGAAAGCCGTCGGACTCGGTGGTTGGCATTGGCTGgtgagcaaagatcaacttcgctttcttctttacctcgttttgtcttttttgcatctttgtgtctgtctgtgtttttattcccccagtagagtagattttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA