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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCATGGAGGGTGCCTATAACCGTGTGTTGAGTGCTAGACAGACCGCGCCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaatgagtctgtccttctctgaattagttcagtcttatgtcttctcgcgtgttatctcacctttttattgttatgactgaattcacag

Basic information

species Arabidopsis thaliana
transcript AT1G64520.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64520.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv02s0025g02010.t01 (Vitis vinifera), 5'ss of exon 4
CCTTCATGGAGGGTGCCTATAACCGTGTGTTGAGTGCTAGACAGACCGCGCCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaatgagtctgtccttctct-gaattagttcagtcttatgtcttctcgcgtgttatctcacctttttattgttatgactgaattcacag-------
| |||||||| || || || || ||||||||||||||||||||||| | |||  ||| |||||| || ||||||||||||||  |||| |||||  | |||||  | |  ||| |    |||      |   |   | | | | | |   | |     | || |  |||     |        || || ||  ||        
CTTTCATGGAAGGAGCTTACAATCGTGTGTTGAGTGCTAGACAGACAGTGCCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactttgacttgagcctctagaaggggttaataaatttcaggaaatttaaaacgataaccaaccac---acacaagccaccgactttgcatattttcc
















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|116486366|gb|EG528958.1|EG528958
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|116486373|gb|EG528965.1|EG528965
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|116486364|gb|EG528956.1|EG528956
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|116478804|gb|EG521396.1|EG521396
EST:     CTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|116486368|gb|EG528960.1|EG528960
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|116446013|gb|EG488605.1|EG488605
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|116486371|gb|EG528963.1|EG528963
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|116486376|gb|EG528968.1|EG528968
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|116486365|gb|EG528957.1|EG528957
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|163993785|gb|ES195785.1|ES195785
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTA
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTA
EST: gi|116486359|gb|EG528951.1|EG528951
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|124948106|gb|EL023895.1|EL023895
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGA
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGA
EST: gi|116486357|gb|EG528949.1|EG528949
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
EST: gi|116478803|gb|EG521395.1|EG521395
EST:     CCTGATGCAACTTACGTTTATTTCATGGATTTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATG
EST: gi|116486361|gb|EG528953.1|EG528953
EST:     CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAG                         AGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG
genomic: CCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaa ... gaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCATGGAGGGTGCCTATAACCGTGTGTTGAGTGCTAGACAGACCGCGCCTGATGCAACTTACGTCTATTTCATGGATCTCTTGGCAAAGACCATAAGgtagcatcaatgagtctgtccttctctgaattagttcagtcttatgtcttctcgcgtgttatctcacctttttattgttatgactgaattcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG