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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaggtttcagatagatacattttcgtttgaatttttgataagctttttggatccaaacagtttcaaatatgtgcagGGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGGAAACAACTATGGGAACTCTGCAAAGACAAGTACGAGCCGCTCTGGGTGAAAGGAGGGAACCACT

Basic information

species Arabidopsis thaliana
transcript AT3G01690.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G01690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g18860.1 (Oryza sativa), 3'ss of exon 4
--------------------gtaagtcaggtttcagatagatacattttcgtttgaatttttgataagctttttggatccaaacagtttcaaatatgtgcagGGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGGAAACAACTATGGGAACTCTGCAAAGACAAGTACGAGCCGCTCTGGGTGAAAGGAGGGAACCACT
                     ||  | |  ||    || |  | | |   |  || ||   |||  |  || || | || || |  ||||     | ||||||||||| | ||||| ||||| ||||| |||||||| || ||||||||||| || |||||||| || || |||||  | ||| | || |||||||| ||||
ctgataggccagtatcaagtttacttgaaattgtgcattg-cataatcctgcatgtatgcctgaatattttattag-tctaatctctttcctccctctgcagGGAACTGCTGATGAAGTAGTTGATTGGTCTCATGGTAAGCAACTATGGGAGCTTTGCAAAGAGAAATATGAGCCTTTATGGCTCAAGGGAGGGAAGCACT

upper sequence: AT3G01690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G039214_T01 (Zea mays), 3'ss of exon 4
-------------------gtaagtca-ggtttcagatagatacattttcgtttgaatttttgataagctttttggatccaaacagtttcaaatatgtgcagGGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGGAAACAACTATGGGAACTCTGCAAAGACAAGTACGAGCCGCTCTGGGTGAAAGGAGGGAACCACT
                     |  ||  ||||| |  |    | || |  |  ||  | ||||||    |  | |    || |   | |     |  || |||||||| | ||||| || |||||||| |||||||| |||||||| |||||||| |||||||||||||| |||||  | ||| | |  ||||| || ||||
tttttttacattaacttgaacatttcttggtttaatttgctcaaatctatgcatgc-tatttgattcattactggtgctcata-gctcttgctgaaatgtagGGAACTGCTGATGAAGTGGTGGATTGGTCTCATGGTAAACAACTTTGGGAACTTTGCAAAGACAAGTATGAGCCCTTATGGCTCAGGGGAGGAAAGCACT

upper sequence: AT3G01690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0219g00290.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtaagtcaggtttcagatagatacattttcgtttgaatttttgat-aagctttttggatccaaacagtttcaaatat----gtgcagGGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGGAAACAACTATGGGAACTCTGCAAAGACAAGTACGAGCCGCTCTGGGTGAAAGGAGGGAACCACT
              |   | |   |  || | |    || |  | |   ||||||  | || | | ||  ||    |   ||| | || |    ||| |||||||||| ||||| ||||| |||||||| ||||| || ||||| |||||||| || ||||| ||||| || || || ||| | ||||||||||||||||
ttatgagagctacatctattaacataaagttgggactatctcagatgttatttttatttaaacctcttttattttgattattttatatctttttgtgtagGGAACTTCAGATGAAGTAGTTGATTGTTCCCATGGCAAGCAACTCTGGGAACTGTGTAAAGAGAAGTATGAACCTCTATGGCTTAAAGGAGGGAACCACT

upper sequence: AT3G01690.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ19908 (Selaginella moellendorffii), 3'ss of exon 4
----------gtaagtcaggtttcagatagatacattttcgtttgaa--tttttgataagctttttggatccaaacagtttcaaatatgtgcagGGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGGAAACAACTATGGGAACTCTGCAAAGACAAGTACGAGCCGCTCTGGGTGAAAGGAGGGAACCACT
          | | |  |||  | || |  |  |  || | | |||   ||||   |   || ||| ||| |      || |   | |  ||||||||| |||||||| || |||||||| || ||||| || || || ||||| ||||||||||| |||                                  
gtaggtgatgggatggaagggattagttccactccattccctctgagagttttctttgtcctcttttgattc---tctttgcgtgtttcggcagGGAACCTCGGATGACGTTGTGGATTGCTCGCATGGAAAGCAGCTCTGGGACCTCTGCAAAGAGAAG----------------------------------

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|125289433|gb|EL303518.1|EL303518
EST:     AATATCGACAAAATCCCATATGTCGATTGCCCGGTTCTCATCATTCAT                         GGAACTTCGGATGAGGTAGT
genomic: AATATCGACAAAATCCCATATGTCGATTGCCCGGTTCTCATCATTCATgtaagtcagg ... atatgtgcagGGAACTTCGGATGAGGTAGT
EST: gi|125269399|gb|EL283484.1|EL283484
EST:     TATGTCGATTGCCCGGTTCTCATCATTTCAT                         GGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGGAAACAACTATGGGA
genomic: TATGTCGATTGCCCGGTTCTCATCA-TTCATgtaagtcagg ... atatgtgcagGGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGGAAACAACTATGGGA
EST: gi|124902131|gb|EH976211.1|EH976211
EST:     AATATCGACAAAATCCCATATGTCGATTGCCCGGTTCTCATCATTCAT                         GGAACTTCGGATGAGGTAGTGGATTGTCCTCATGGG
genomic: AATATCGACAAAATCCCATATGTCGATTGCCCGGTTCTCATCATTCATgtaagtcagg ... atatgtgcagGGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtttgaatttttgataagctttttggatccaaacagtttcaaatatgtgcagGGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGGAAACAACTATGGGAACTCTGCAAAGACAAGTACGAGCCGCTCTGGGTGAAAGGAGGGAACCACT
           ttttgat  putative branch site (score: 4)
     ttgaatttttgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaggtttcagatagatacattttcgtttgaatttttgataagctttttggatccaaacagtttcaaatatgtgcagGGAACTTCGGATGAGGTAGTGGATTGTTCTCATGGGAAACAACTATGGGAACTCTGCAAAGACAAGTACGAGCCGCTCTGGGTGAAAGGAGGGAACCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG