Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtttttcctgtttaaagaatgcatcctttagtgttttttaaatatagcttgcttcatgttttttttcttttcctttttgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTTGACCGTGAAGCTGAAGATCCTGCTGTACGCCTTGCTTTGGGAGAAACAA

Basic information

species Arabidopsis thaliana
transcript AT4G19610.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G19610.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G09970.1 (Glycine max), 3'ss of exon 8
-gtacgtttttcctg-------tttaaagaatgcatcctttagtgttttttaaatatagcttgcttcatgttttttttcttttcctttttgtgttg-tagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTTGACCGTGAAGCTGAAGATCCTGCTGTACGCCTTGCTTTGGGAGAAACAA
  |   || |||||        | | || |||||   |||| |  || |     |  |  |   |  || | | ||||       |||   ||||  ||| || | |||||||| | | ||   | |||||| || || ||||| ||||||||||| |||||||| |||| |||||||||  ||||||||||||| ||  
tcttttttcttcctaaaatgtttcttaaaaatgctctcttttgctttatggttgtgcatttccttgtatatatattttaggcatgtttcgctgttaatagGTTGTGGAAAACATTGCCCGGAAATTTGGTGTTAGTAAAAGTGATTTACTTGACCGAGAAGCTGATGATCTTGCTGTACGTATTGCTTTGGGAGAGACTC
















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|116458756|gb|EG501348.1|EG501348
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116458749|gb|EG501341.1|EG501341
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116413076|gb|EG455668.1|EG455668
EST:     GTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: GTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116413073|gb|EG455665.1|EG455665
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116413069|gb|EG455661.1|EG455661
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116413075|gb|EG455667.1|EG455667
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116458754|gb|EG501346.1|EG501346
EST:     CTGGTGGAGATACAAAGGCTTGGGATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116413074|gb|EG455666.1|EG455666
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116458748|gb|EG501340.1|EG501340
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116458745|gb|EG501337.1|EG501337
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116413072|gb|EG455664.1|EG455664
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
EST: gi|116413070|gb|EG455662.1|EG455662
EST:     CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACT                         ATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT
genomic: CTGGTGGAGATACAAAGGCTTGGAATAGTTTATTCATGCGACCCGATACTgtacgttttt ... tgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttaaatatagcttgcttcatgttttttttcttttcctttttgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTTGACCGTGAAGCTGAAGATCCTGCTGTACGCCTTGCTTTGGGAGAAACAA
               cttgcttcatgttttt  CT-rich tract
                       atgttttttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtttttcctgtttaaagaatgcatcctttagtgttttttaaatatagcttgcttcatgttttttttcttttcctttttgtgttgtagATTCTAGAAAACATAGTCAGGGTGTATGGTGTAAGCAAGAGTGAGTTACTTGACCGTGAAGCTGAAGATCCTGCTGTACGCCTTGCTTTGGGAGAAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA