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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgtttttgttattttcatatgtctcatcatcaaaatgtctgcaagttcttcattggctttactgggccgtcttttcttatgtgtttttttttatgccatagATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAG

Basic information

species Arabidopsis thaliana
transcript AT4G21790.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G01820.1 (Glycine max), 3'ss of exon 7
------------------gtctgt-gtttttgttat----tttcatatgtctcatcatcaaaatgtctgcaagttcttcattggctttactgggccgtcttttcttatgtgtttttttttatgccat-agATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAG
                  |||||| || | ||  ||      ||  | ||||| |  |  |        |  ||  ||||| |   ||| ||||    |||||    |    | |  |  |||   | ||||| ||||||||||| ||| | ||||| || || || ||||||||||||||||||||| | |||
gtgaggcttctgcattttgtctgttgtctatgaaataatacctctgaggtctcctgtttcattcactcactggtaattcatggttgtta-tgggtgaactttttgatttccctgtggtaaatgtttttagATTATTTTTCATGCTGAGACGCTTCCCAATTGAATCTAAAGGAAGAAGGAAGAAACTCAATGAG

upper sequence: AT4G21790.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G38920.2 (Glycine max), 3'ss of exon 7
-------gtctgtgtttttgttattttcatatgtctcatcatcaaaatgtctgcaagttcttcattggctttactgg--gccgtcttttcttatgtgt----ttttttttatgcca-tagATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAG
        ||||  ||||   |||      ||  ||| | |      ||| |    ||  ||||| |   |||  ||   || | |||  |||  |||       |||  |||    |||||| ||||||||||| ||  | ||||| || || || ||||||||||||||||||||| | |||
gtaaggcttctgcattttgtctatgaaataatacctc-tgaggtctctgtttcattgtaattcatggttgttatgggtaaccttttttatttacctgtggaacactttaaatgtttctagATTATTTTTCATGCTGAGGCGCTTCCCAATTGAATCTAAAGGAAGAAGGAAGAAACTCAATGAG
















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|124790912|gb|EH880591.1|EH880591
EST:     GCCGCATTAGGCTTCTTGCTGTATGGAGGAAG                         ATTGTTTTTCATGCTAAGAAGGTTCCCCATCGAGTCAAAAGGAAGAAGGAA
genomic: GCCGCATTAGGCTTCTTGCTGTATGGAGGAAGgtctgtgttt ... tatgccatagATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAA
EST: gi|86078543|gb|DR374300.1|DR374300
EST:     TTGTGTCTTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAG                         ATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAA
genomic: TTGTGTCTTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAGgtctgtgttt ... tatgccatagATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAA
EST: gi|125253411|gb|EL267496.1|EL267496
EST:     TCTTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAG                         ATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAA
genomic: TCTTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAGgtctgtgttt ... tatgccatagATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAA
EST: gi|164034477|gb|ES097267.1|ES097267
EST:     TTGTG-CTTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAG                         ATTGTTTT-CATGCTAAGAAGGTTCCCTATCGAGTCAAAAGG
genomic: TTGTGTCTTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAGgtctgtgttt ... tatgccatagATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGG
EST: gi|124975892|gb|EL049351.1|EL049351
EST:     TTGTGTCTTTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAG                         ATTGTTTTTACATGCTAAGAAGGTTCCCTATCGAGTCAAA
genomic: TTGTGTC-TTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAGgtctgtgttt ... tatgccatagATTGTTTTT-CATGCTAAGAAGGTTCCCTATCGAGTCAAA
EST: gi|125276844|gb|EL290929.1|EL290929
EST:     TTGTGTCTTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAG                         ATTTGTTTTTCATGCTAAGAAGGTTCCCTATC
genomic: TTGTGTCTTTCATCGCCGCATTAGGCTTCTTGCTGTATGGAGGAAGgtctgtgttt ... tatgccatagATT-GTTTTTCATGCTAAGAAGGTTCCCTATC
EST: gi|125184027|gb|EL198981.1|EL198981
EST:     CTTCTTGCTGTATGGAGGAAG                         ATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAA
genomic: CTTCTTGCTGTATGGAGGAAGgtctgtgttt ... tatgccatagATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcattggctttactgggccgtcttttcttatgtgtttttttttatgccatagATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAG
                       tcttttcttatgtgtt  CT-rich tract
                         ttttcttatgtgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtgtttttgttattttcatatgtctcatcatcaaaatgtctgcaagttcttcattggctttactgggccgtcttttcttatgtgtttttttttatgccatagATTGTTTTTCATGCTAAGAAGGTTCCCTATCGAGTCAAAAGGAAGAAGGAAGAAACTCCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA