Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgctcttcttttgttccacatgttctcaagtttgatattagctttttgttgggctgagttttttagaatcttcgttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTTGATTGAATATGAAAAAACCGAATACACGGATGTATTTGGAAGAGCAAGG

Basic information

species Arabidopsis thaliana
transcript AT5G64250.2
intron # 3
splice site 3'
intron type U2

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|116453508|gb|EG496100.1|EG496100
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453507|gb|EG496099.1|EG496099
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453498|gb|EG496090.1|EG496090
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453517|gb|EG496109.1|EG496109
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453516|gb|EG496108.1|EG496108
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453512|gb|EG496104.1|EG496104
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453501|gb|EG496093.1|EG496093
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453499|gb|EG496091.1|EG496091
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453500|gb|EG496092.1|EG496092
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453502|gb|EG496094.1|EG496094
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|86039414|gb|DR335169.1|DR335169
EST:     ATGTTGCAGCTTTGTCACTTGGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATA
genomic: ATGTTGCAGCTTTGTCACTTGGGG-CTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATA
EST: gi|116453497|gb|EG496089.1|EG496089
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453511|gb|EG496103.1|EG496103
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
EST: gi|116453503|gb|EG496095.1|EG496095
EST:     TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAG                         ATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT
genomic: TATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgtgtgctc ... gttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgatattagctttttgttgggctgagttttttagaatcttcgttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTTGATTGAATATGAAAAAACCGAATACACGGATGTATTTGGAAGAGCAAGG
 gtttgat  putative branch site (score: 5)
                                        tcttcgttttctt  putative PPT
                              ttttttagaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgctcttcttttgttccacatgttctcaagtttgatattagctttttgttgggctgagttttttagaatcttcgttttcttagATTTGTGGCGACTCATGAAAGCTATGCACACCCAATATACAAAAGGAAGTTGATTGAATATGAAAAAACCGAATACACGGATGTATTTGGAAGAGCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG