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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatattatacattgtagagtttcggttatgatgaaccattttattttgattgatcagttttcattattacttcgaaataacatttaatctgataacaactgttgattttctacccgtagCCACTGTTTCCCGGGGAAAGTGGCATTGATCAGCTGGTGGAGATAATCAAG

Basic information

species Arabidopsis thaliana
transcript AT4G00720.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtatattatacattgtagagtttcggttatgatgaaccattttattttgattgatcagttttcattattacttcgaaataacatttaatctgataacaactgttgattttctacccgtagCCACTGTTTCCCGGGGAAAGTGGCATTGATCAGCTGGTGGAGATAATCAAG
            | |||| |    ||| |  |||||||  || |  ||| ||  ||  | |  |||||| |  |  |   | |        || || ||     |||||   |  ||   | ||||||||||||| |||||||||||  |||||||||||||||| || || |||
-----------gttcattttc--ttttggtctatgatgtgcc-tcatatcttcctt--ttatctttcatgaacatgttacatttctgaccgatatgcta-----tgttg---tgttatgtgcagCCACTGTTTCCTGGGGAAAGTGGTGTTGATCAGCTGGTGGAAATCATTAAG
















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|124708108|gb|EH799510.1|EH799510
EST:     TTGACATGTGGTCCGGCGGTTGTGTCATGGCAGAGCTTTTACTTGGTCAA                         CCACTGTTTCCCGGGGAAAGTGG
genomic: TTGACATGTGGTCCGGCGGTTGTGTCATGGCAGAGCTTTTACTTGGTCAAgtaagtatat ... ctacccgtagCCACTGTTTCCCGGGGAAAGTGG
EST: gi|124969671|gb|EL043559.1|EL043559
EST:     TTGACATGTGGTCCGGCGGTTGTGTCATGGCAGAGCTTTTACTTGGTCAA                         CCACTGTTTCCCGGGGAAAGTGGACATTGATCAGCTGGTGGAGA
genomic: TTGACATGTGGTCCGGCGGTTGTGTCATGGCAGAGCTTTTACTTGGTCAAgtaagtatat ... ctacccgtagCCACTGTTTCCCGGGGAAAGTGG-CATTGATCAGCTGGTGGAGA
EST: gi|164203535|gb|ES138960.1|ES138960
EST:     TTGACATGTGGTCCGGCGGTTGTGTCATGGCAGAGCTTTTACTTGGTCAA                         CCACTGTTTCCCGG
genomic: TTGACATGTGGTCCGGCGGTTGTGTCATGGCAGAGCTTTTACTTGGTCAAgtaagtatat ... ctacccgtagCCACTGTTTCCCGG
EST: gi|125163843|gb|EL190613.1|EL190613
EST:     TTGACATGTGGTCCGGCGGTTGTGTCATGGCAGAGCTTTTACTTGGTCAA                         CCACTGTTTCCCGGGGAAAG
genomic: TTGACATGTGGTCCGGCGGTTGTGTCATGGCAGAGCTTTTACTTGGTCAAgtaagtatat ... ctacccgtagCCACTGTTTCCCGGGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattacttcgaaataacatttaatctgataacaactgttgattttctacccgtagCCACTGTTTCCCGGGGAAAGTGGCATTGATCAGCTGGTGGAGATAATCAAG
                                         ttttctaccc  CT-rich tract
          aaataacatttaatct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatattatacattgtagagtttcggttatgatgaaccattttattttgattgatcagttttcattattacttcgaaataacatttaatctgataacaactgttgattttctacccgtagCCACTGTTTCCCGGGGAAAGTGGCATTGATCAGCTGGTGGAGATAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT