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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttggaatttcagaacttaaaaaactagataacagtttgcaaaatggtacactggattagcagtttttaagcattttttatgaaacctgaatgtt...

Basic information

species Arabidopsis thaliana
transcript AT3G53580.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: AC182617.3_FGT001 (Zea mays), 5'ss of exon 8
GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttggaatttcagaacttaaaaa-actagataacagtttgcaaaatggtacactggattagcagtttttaagcattttttatgaaacctgaatgtt---------------------
|||||||| | |||||||| ||||| ||||||||  ||||||||||||| || ||||| |||||||| ||  ||||  ||      || |      |       |||  |     |||     ||| | ||          ||||| ||     ||||| | | |||| | | ||                     
GAGCAACTCTTGCCTGTGGTACTGGTGCTTGTGCAGTGGTTGTTGCAGCTGTTCTTGAGGGTCGAGCTGAGCGGgtttgtcattctttcctttctgtgtgtttgctattttggcatttcactcatgattcatattcactatagtttatag----tttttgttataccttattctttaactttttatcatgaaacag

upper sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G130332_T03 (Zea mays), 5'ss of exon 8
GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagttt---ggaatttcagaacttaaaaaactag-ataacagtt---tgcaaaatggtacactggat-tagcagtttttaagcattt-tttatgaaacctgaatgtt
|||||||| |  ||||||| ||||| ||||||||  ||||||||||||| || ||||| |||||||| ||  ||||  || |        ||  |   ||       | | ||  || |    |  |  |  ||  |  |  | |   |    || | | ||| ||| |  || |  ||    
GAGCAACTCTTACCTGTGGTACTGGTGCTTGTGCGGTGGTTGTTGCAGCTGTTCTTGAGGGTCGAGCTGAGCGGgtttgtctttcttgccttttgtgtttgcttttttggcatttcactcatatttactacagtctatagtttgtgttataccttgatcttttatttttttaatcataacag-

upper sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA03G33080.1 (Glycine max), 5'ss of exon 9
GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttggaatttcagaacttaaaaaactagataacagtttgcaaaatggtacactggattagcagtttttaagcatt-ttttatgaaacctgaatgtt--
|||||||  | ||||||||||||||||||||||||   |||||||||||||| ||||| ||||| || |  ||||||||||||    ||     |||  || | ||   ||    |||       ||   |  |    ||  | |  ||    | ||  ||   || |   ||||  
GAGCAACCCTAGCCTGTGGAACTGGAGCTTGTGCTACTGTTGTTGCAGCAGTTCTTGAGGGTCGTGCTGGGAGGgtaagtttgctgctt---gtcttgtaacaatatgaaaactattgattttctgtgtgcctgtgcggcgctatgcaaatgctattgcattgcacttttgtgttgt

upper sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA19G35780.1 (Glycine max), 5'ss of exon 8
GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttggaatttcagaacttaaaaaactaga-----taacagtttgcaaaatggtacactggattagcagtttttaagcattttttatgaaacctgaatgtt
|||||||  | ||||||||||||||||||||||||   |||||||||||||| ||||| ||||| || |  ||||| ||||||  | ||  | | | | || |  | |     | |   | |   ||||  |     | | |   |||  | ||   |   |  | |     |  ||| 
GAGCAACCCTAGCCTGTGGAACTGGAGCTTGTGCTACTGTTGTTGCAGCAGTTCTTGAGGGTCGTGCTGGGAGGgtgagtttgctacttttgtagtaacaatatgaaacatattgattttctattaaattttttttcgtaatcatagtagtcaatagtgactggtta-----gcgtgtc

upper sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv08s0040g02540.t01 (Vitis vinifera), 5'ss of exon 8
GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagttt---ggaatttcagaac-ttaaaaaactagataacagtttgcaaaatggtacactggattagcagtttttaagcattttttatgaaacctgaatgtt-
|||||||| | |||||||||||||||||||||||  |||||||||||||||| ||||| ||||  || |  |||||||||||   |   ||| | ||  || |  || |   |    |||    |  |   ||   |||     |       ||||  |||| |  |     |||| | 
GAGCAACTCTAGCCTGTGGAACTGGAGCTTGTGCAGTGGTTGTTGCAGCAGTTCTTGAGGGTCATGCTGGGAGGgtaagtttcccgatgtttaaaaatattgaggaattcact--tggttctttagttatcactgaggacagaaaac---agagcagattttttagatatcaaatgatt

upper sequence: AT3G53580.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: PP1S51_241V6.1 (Physcomitrella patens), 5'ss of exon 9
GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttggaatttcagaacttaaa----aaactagat-aacagtttgcaaaatggtacactggattagcagtttttaagcattttttatgaaacctgaatgtt
| || |||  ||||||||||||||||||||||||  | |||||||| |||||    |||||||| ||||| ||||| |||| |    | | | | |  ||     | |||||| ||   | |     ||  |   || |  |  ||||  |    |   |||  |||||   |      
GTGCTACTCAGGCCTGTGGAACTGGAGCTTGTGCGGTAGTTGTTGCTGCAGTGAAGGAAGGTCGCGCCGAAAGGgtgagttcgtgtgtcctgtaatgcaatcttgagctagatgaatcatcttgtgtatcttgttcttggatgacagtggtgttcctaatttgttgaaaatggc-----

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|86086855|gb|DR382614.1|DR382614
EST:     GAGCTTGTGCTCTGGTTGTTGCASCAGTCCTTDAAGGTCGAGCCGACAGG                         AAATGCMCGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|124831382|gb|EH915821.1|EH915821
EST:     TTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: TTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|125157755|gb|EL186678.1|EL186678
EST:     TTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: TTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|86082085|gb|DR377844.1|DR377844
EST:     GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|86080834|gb|DR376591.1|DR376591
EST:     GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|86065678|gb|DR361435.1|DR361435
EST:     GCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: GCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|124811007|gb|EH895873.1|EH895873
EST:     CAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: CAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|86078439|gb|DR374196.1|DR374196
EST:     GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|125130598|gb|EL173732.1|EL173732
EST:     CTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: CTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|116478499|gb|EG521091.1|EG521091
EST:     GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
EST: gi|124929173|gb|EL006745.1|EL006745
EST:     GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATA
genomic: GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATA
EST: gi|116478497|gb|EG521089.1|EG521089
EST:     GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGG                         AAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG
genomic: GAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttgg ... ggtggaacagAAATGCACGGTGGATCTACCGGGCGGACCATTGGAGATAGAGTGGAAACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCAACTTTGGCCTGTGGAACTGGAGCTTGTGCTCTGGTTGTTGCAGCAGTCCTTGAAGGTCGAGCCGACAGGgtaagtttggaatttcagaacttaaaaaactagataacagtttgcaaaatggtacactggattagcagtttttaagcattttttatgaaacctgaatgtt

- - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agataaca