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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaataccatttctcaagactcttggttcccattttcttgaacagaataataaaaccttaagcttcttctgtgttggccttccttttgcag

Basic information

species Arabidopsis thaliana
transcript AT3G02780.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G02780.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 5
CTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaataccatttctcaagactct---tggt----tcccattttcttgaacagaataataaaaccttaagcttcttctgtgttggc-----cttccttttgcag---------------------------------
|| || ||   |||||||||  |||| || ||  | |||| |||  | ||  | ||||| ||||||||||| |||||||| |||||||| || ||||||||||||||      |||    ||||   || |    | |    ||| |    |   |      | |    || |||| ||| ||  |     ||  |||||| |                                  
CTGGGAATACAAGCTGAAGAACTACCTGTTGACCAATTCATTCCTCTTGGGAGGATGCTTTACAAGGCTCCATCTGATGGAAAATGGGGCGAACATGAACgtaaatatttgccctctgccctctacctgatacatttcagccttcatacttatcgtccagctatcacttgcctcttgtgtattttcaattgctgtcttttgaaatttttagaatataaccatctttcgccatttcag

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA09G38550.1 (Glycine max), 5'ss of exon 5
CTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaa----ataccatt--tctcaagactcttggtt--cccattttcttgaacagaataataaaacc--ttaagcttcttctgtgttggccttccttttgcag
||||||||||| || |||||||||||||| ||| ||||||| |||||||| || || || |||||||| |||||||||||||||||||||||||||||||||||    ||   |||  | |||||  |    |    |  | ||| ||| | |    | ||       || |   |  | |   | ||| || |        
CTTGGTATTGTTGCCGAAGATGTACCAGTTGATAAGTTCACCCCCTTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaatttaattgatttcaagttttgcagcaagcttaattttttgtataaccaactagggttaattcacactaatttaattaggcattgcaaacat--

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 5
CTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaataccatttctcaagactcttggttc-----ccattttcttgaacagaataataaaaccttaagcttcttctgtgttggccttccttttgcag---------
 |||||||||| ||||||||||||||||| ||| ||||||| || ||||| || || || |||||||| ||||||||||||||||||||||||||||||||| |   ||| ||     || |  | |||      | |  || ||     | ||||  ||    || | ||  |      |    |      ||||          
-TTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACGtgag--ccaatttaattgatttctagttttacagcaagcttattttgttgtataaccaa---ctagggttaattcacactaatttaaggaatgcaaacataaatc

upper sequence: AT3G02780.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 5'ss of exon 5
CTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaataccatttctcaagactcttggttcccattttcttgaacagaataataaaaccttaagcttcttctgtgttggccttccttttgcag---------------
|| || |||   |||||||||| ||| || ||| ||||||||||  |||| || ||||| |||||||| || || |||||||| ||||||||||||||||||||  | |    ||        ||  || | | | ||   ||| || | |||      |  | ||   |||| |          | || ||               
CTCGGCATTCCTGCTGAAGATGCACCTGTTGATCAGTTCACTCCACTGGGCCGCATGCTTTACAAGGCACCATCAGATGGCAAGTGGGGAGAGCATGAACgtaataatctgaactttga----tttatttcaaatctc---aactgatttatatggtgctttgttttaactgtttcataaagttgtctgaagctttgagccagggtc

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|47828035|gb|CK117719.1|CK117719
EST:     ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAG
genomic: ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaatacca ... ccttttgcagTTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAG
EST: gi|164120867|gb|ES058913.1|ES058913
EST:     GGGGAGAGCATGAAC                         TTGATTACTTGCTCTTCATTGTGCGAGACGTGAAGGTTCAACCAAACCCAG
genomic: GGGGAGAGCATGAACgtaaatacca ... ccttttgcagTTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAG
EST: gi|116477195|gb|EG519787.1|EG519787
EST:     ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGGAC                         TTGATTACTTGCTTTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAG
genomic: ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaatacca ... ccttttgcagTTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAG
EST: gi|116387556|gb|EG430148.1|EG430148
EST:     ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAG
genomic: ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaatacca ... ccttttgcagTTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAG
EST: gi|124806885|gb|EH893446.1|EH893446
EST:     ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACC
genomic: ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaatacca ... ccttttgcagTTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACC
EST: gi|116477196|gb|EG519788.1|EG519788
EST:     ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGGAC                         TTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAG
genomic: ACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaatacca ... ccttttgcagTTGATTACTTGCTCTTCATCGTGCGAGACGTGAAGGTTCAACCAAACCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTACAAGGCTCCTTCTGATGGCAAATGGGGAGAGCATGAACgtaaataccatttctcaagactcttggttcccattttcttgaacagaataataaaaccttaagcttcttctgtgttggccttccttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA