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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttggcataaattttcagtttattcccaactatatatgtttgattatgcaatggcatattccttttgcattatgtgaataactttgtttgtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAACAGGAGGACTGTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G26880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G26880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 2
-ctttggcataaattttcagtttattcccaactatatatgtttgattatgcaatggcatattccttttgcattatgtgaataactttgtttgtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAACAGGAGGACTGTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAG
  |   |  |   | ||||  |||     |    | |    |    |||   |  | |||||  |  |  |  || |  | |   || | | ||| | ||||| || |||||||||||  |||||||||||||||| || || || || ||| | |||||||| |||||  |||| ||||||||  | |||||  ||||||
gataccgtttggttcttcatattaccgatattacttttctctatgctatttcactggatatttgtacttgaggatttatacagtgttctat-tttctccagATTCCCCACTTGAGGCCTGCTGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTGAACCGTCCATATGGTGGAGTGCTCTCTGGAACTGCAG

upper sequence: AT1G26880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g06040.1 (Oryza sativa), 3'ss of exon 2
----ctttggcataaattttcagtttattcccaactatatatgtttgattatgcaatggcatattccttttgcattatgtgaataactttgtttgtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAACAGGAGGACTGTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAG
      |||  |||| |||||  |  |     | ||   || | || ||| |  ||      | |    |||  |  |   ||     ||||       | ||||| || ||| |||| ||  |||||||||||||||| ||||| ||||| ||  | ||||| || |||||  | |||||||| ||| |||||||| ||||||
aattggttgaaataagttttctttgaaccggtatct---taagcttcattgt-taacattgcaatatccttggttcttacaaagttgcttgtgctaaactgcagATTCCACACCTGAGACCTGCTGAGTACAAGAGGTCCAGATTGTCAAGGAATCGCAGGACCGTGAACCGTCCTTACGGTGGTGTCCTGTCTGGTACTGCAG

upper sequence: AT1G26880.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 2
--ctttggcataaattttcagtttattcccaactatatatgtttgattatgcaatggcatattccttttgcattatgtgaataactttgtttgtttatt--cagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAACAGGAGGACTGTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAG
  | |   || |     ||||| |   |  ||||   |||  |    | |     |  || | |   |   ||| | | |||    ||||||   ||||  ||||||||||||||||||||  |||||||||| ||||| || ||  | || | | | |||||||| |||||  | || ||||||||  | |||||   ||| |
tacctgaaca-atgccctcagtgtcaccaaaactgggtat--tcatctgtcattggatatttccacctaatattgttt-aatgctattgtttccatatttccagATCCCTCACTTGAGGCCTGCTGAGTACAAAAGGTCCAGGTTGCCTAGGAGCCGCAGGACTGTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTG

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|124722125|gb|EH813527.1|EH813527
EST:     AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGA                         ATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAG
genomic: AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGAgtaagtcttc ... gtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAG
EST: gi|164033259|gb|ES013957.1|ES013957
EST:     GCGTATTCAAGGA                         ATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGAT
genomic: GCGTATTCAAGGAgtaagtcttc ... gtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGAT
EST: gi|125187721|gb|EL202675.1|EL202675
EST:     AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGA                         ATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCA
genomic: AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGAgtaagtcttc ... gtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCA
EST: gi|86075408|gb|DR371165.1|DR371165
EST:     AGAAAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGA                         ATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC
genomic: AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGAgtaagtcttc ... gtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC
EST: gi|163967721|gb|ES055426.1|ES055426
EST:     CGTATTCAAGGA                         ATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC
genomic: CGTATTCAAGGAgtaagtcttc ... gtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC
EST: gi|86081954|gb|DR377713.1|DR377713
EST:     AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGA                         ATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC
genomic: AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGAgtaagtcttc ... gtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC
EST: gi|164116897|gb|ES036126.1|ES036126
EST:     AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGA                         ATCCCTCACTTG
genomic: AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGAgtaagtcttc ... gtttattcagATCCCTCACTTG
EST: gi|164053813|gb|ES151707.1|ES151707
EST:     GGCAAGCGTATTCAAGGA                         ATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC
genomic: GGCAAGCGTATTCAAGGAgtaagtcttc ... gtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC
EST: gi|86081699|gb|DR377456.1|DR377456
EST:     AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGA                         ATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC
genomic: AGAGAGCTAGTGGCCCCAAATGTCCTGTTACTGGCAAGCGTATTCAAGGAgtaagtcttc ... gtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcaatggcatattccttttgcattatgtgaataactttgtttgtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAACAGGAGGACTGTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAG
                               gaataac  putative branch site (score: 2)
                                          tttgttt  putative PPT
                                      tttgtttgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttggcataaattttcagtttattcccaactatatatgtttgattatgcaatggcatattccttttgcattatgtgaataactttgtttgtttattcagATCCCTCACTTGAGGCCCTCTGAGTACAAGAGGTCAAGATTATCAAGAAACAGGAGGACTGTAAACCGAGCATACGGTGGAGTCTTGTCTGGTTCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG