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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaagacactagctaaaatacattgcactagtagcattttatcattacacaaaagcgttatcatcatccgatattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGTGCTTACCATGGTAAATTCTCATTTGATGCTTTTAGTCACAAGAAGGCGG

Basic information

species Arabidopsis thaliana
transcript AT1G44170.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G44170.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G26390.1 (Glycine max), 3'ss of exon 9
-gta-agaaagacactagctaa---aatacattgcactagtagca--ttttatcattacacaaaagcgttatcatcatccgatatttt--------gcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGTGCTTACCATGGTAAATTCTCATTTGATGCTTTTAGTCACAAGAAGGCGG
  || |||    ||| |  | |   |||   ||| | || |  ||  | | | || ||  ||   | |||   ||  |||    ||||        |||||||||| |||| || || ||||| || ||||||||||| |||||| ||||||| |||||||| |||||||||||||| |||||||| ||||| || || |
tctatagatgctcacaattttatttaatgttttgaaataatttcaagtgtgaacactattcacccgtgtttctattttccatcttttttgcctggtgcagCTTGCAGTTCATACTTTACCATTTGGTGGAGTTGGTGAGAGTGGAGTGGGTGCATACCATGGGAAATTCTCATTTGAAGCTTTTAGCCACAAAAAAGCTG

upper sequence: AT1G44170.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA14G24140.1 (Glycine max), 3'ss of exon 9
--------gtaagaaagacactagct-aaaatacattgca-ctagtagcattttatcattaca-----caaaagcgttatcatcatccgatattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGTGCTTACCATGGTAAATTCTCATTTGATGCTTTTAGTCACAAGAAGGCGG
          ||   |   | |   |  |||||  ||  | ||     |  || |||| |              || | |   | |      |  ||||||||||| |||| || || ||||| || ||||||||||| |||||| ||||||| |||||||| |||||| ||||||| |||||||| ||||| || || |
agatgctcacaatttatgtattgttttgaaataatttctatctgaacactattcatcactgtgttttttgttttcgatttggcctttttgcctggtgcagCTTGCAGTTCATACTTTACCATTTGGGGGAGTTGGTGAGAGTGGAGTGGGTGCATACCATGGGAAATTCACATTTGAAGCTTTTAGCCACAAAAAAGCAG

upper sequence: AT1G44170.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G12010.1 (Glycine max), 3'ss of exon 9
------------gtaagaaagacactagctaaaatacattgcactagtagcattttatcattacacaa-aagcgttatcatcatccgatattt--tgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGTGCTTACCATGGTAAATTCTCATTTGATGCTTTTAGTCACAAGAAGGCGG
             ||   | |    || |     ||      | |  |    |||| |  | |  ||| || | |    ||  |||  ||  |  |||||||||   || | || |||||||| || |||||||| || |||||||||||||| |||||||| || ||||| |||||||||||||  ||||| ||||| |
attatgatatctatagatatggatataacattgttaatcaatatttcttattttttgttttgaatcaataatcatgtgtattttcctttacctggtgcagCTTGTCGTTGATACTTTGCCATTTGGGGGAGTTGGGGAGAGTGGAATGGGTGCATACCATGGGAAGTTCTCTTTTGATGCTTTTACACACAAAAAGGCAG

upper sequence: AT1G44170.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G42740.1 (Glycine max), 3'ss of exon 9
-------------------gtaagaaagacactagctaaaatacattgcactagtagcattttatcattacacaaaagcgttatcatcatccgatattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGTGCTTACCATGGTAAATTCTCATTTGATGCTTTTAGTCACAAGAAGGCGG
                    |   |||  |  ||  |    |    |       ||  || | | ||||   ||   |  || || |  |||    |  |||||||||   || | || |||||||| || |||||||| || |||||||||||||| |||||||| || ||||| |||||||||||||  ||||| || || |
ataggcattttgcattgttatttaaaaatccttattttctgtttcatatcaacttaaaatctgaacatttttcatgtgtattctccttttcc----tggtgcagCTTGTGGTTGATACCTTGCCATTTGGGGGAGTTGGGGAGAGTGGAATGGGTGCATACCATGGGAAGTTCTCTTTTGATGCTTTTACACACAAAAAAGCAG

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|164232893|gb|ES034279.1|ES034279
EST:     CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCAT                         CTTGCACTTCACACA
genomic: CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCATgtaagaaaga ... tattttgcagCTTGCACTTCACACA
EST: gi|86074378|gb|DR370135.1|DR370135
EST:     CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCAT                         CTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT
genomic: CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCATgtaagaaaga ... tattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT
EST: gi|86076863|gb|DR372620.1|DR372620
EST:     CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCAT                         CTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT
genomic: CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCATgtaagaaaga ... tattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT
EST: gi|86029395|gb|DR325148.1|DR325148
EST:     CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCAT                         CTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT
genomic: CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCATgtaagaaaga ... tattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT
EST: gi|116465913|gb|EG508505.1|EG508505
EST:     CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCAT                         CTTGCACTTCACACATTGCC
genomic: CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCATgtaagaaaga ... tattttgcagCTTGCACTTCACACATTGCC
EST: gi|116465916|gb|EG508508.1|EG508508
EST:     CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCAT                         CTTGCACTTCACACATTGCC
genomic: CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCATgtaagaaaga ... tattttgcagCTTGCACTTCACACATTGCC
EST: gi|86084360|gb|DR380119.1|DR380119
EST:     CAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCAT                         CTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT
genomic: CAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCATgtaagaaaga ... tattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT
EST: gi|116465923|gb|EG508515.1|EG508515
EST:     CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCAT                         CTTGCACTTCACACATTGCC
genomic: CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCATgtaagaaaga ... tattttgcagCTTGCACTTCACACATTGCC
EST: gi|86080652|gb|DR376409.1|DR376409
EST:     CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCAT                         CTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT
genomic: CAGCGACAGTCTCCGCTGGAGGCATAGTAGTCAATGACATAGCTGTTCATgtaagaaaga ... tattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actagtagcattttatcattacacaaaagcgttatcatcatccgatattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGTGCTTACCATGGTAAATTCTCATTTGATGCTTTTAGTCACAAGAAGGCGG
         attttatcattaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaagacactagctaaaatacattgcactagtagcattttatcattacacaaaagcgttatcatcatccgatattttgcagCTTGCACTTCACACATTGCCATTCGGAGGAGTTGGTGAAAGTGGAATGGGTGCTTACCATGGTAAATTCTCATTTGATGCTTTTAGTCACAAGAAGGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG