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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG

Basic information

species Arabidopsis thaliana
transcript AT4G16155.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 9
----------gttagtggagttttct--ttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
             | || | |    |  ||  |  ||  || | ||   |     || |||    |  | |     |  || | ||  ||| ||||||||  |||| || ||||| || ||||||||||||||||| |||||||||||||| || ||||| || ||||| ||||
gtatgttgaaacaaatgaattaccatgctttgttcagaataatcctcttcctggcttgtatgggatctaacatgccatgcatttttatttg-tagGTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
----------------gttagtggagttttctttcatatagcttat--ttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
                |   || | ||||   ||   ||   |||   |   |    |   | ||   ||  |  | || |||     | ||  |    |||||||  | ||||| || || || ||||||||||| ||||| ||||| |||||||| || ||||| |||||||| || |
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgata-tgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 8
---------gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaa---------gctactgagtcactc-ttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
             || | || ||  |     |   || || |||  ||| | |  ||    ||| |         |||||  |  || |    |||    |||||||  | || || || ||||| |||||||||||||| || ||||||||||||||||| || || |||||||| || |
gtatgctaaacctgtagtgtgttactgttactcttttgttcctttacaacaatggtaggcatttcattcaagtttgctacataaacattaaccggtatgcagGTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactc----------ttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
||  || |    || | |   |  | || |||| |   || |  | ||    |  |   | |||  | | ||          ||  |  | |||| ||| | || || ||||| || ||||||||||| || || |||||||| ||||| || ||||| ||||||||||| |
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtac-cctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
gttagtggagttttctttcatata-gcttatttcttaccaaaagttatatatttttaagctactgagtca--ctcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
           ||| ||||||  |  | || || ||       ||   | |  ||   | |||||| | |   | | |  ||||||||||| || ||||| ||||| |||||| | ||||| ||  |||||||||||||||| || ||||| ||||||||||| |
----------gtttgtttcatgaatacataattttttttcttggtctgacacatt---gttactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
||| ||      ||||    ||    ||||  ||  |  |   |||| | ||  | |  ||    ||       |  |||||||| || || || ||||| || |||||||| ||||| ||  |||||||||||||||| || ||||| ||||||||||| |
gtttgtctcaacttctcaagtaataattatccctccctgac--ttat-tgttactgacataggatgtg------gaatgatagGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
-gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
  ||  |  |  | | |     | |  |||||| || |      | | | ||| ||     | | ||  | | | |  ||||||||||| || ||||| || || |||||||| ||||| ||  |||||||||||||||| || || || ||||||||||| |
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgttgc-tgatttag--agtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
||| ||     |||||     |    ||||  ||  |  |   |||| | ||  | |  ||    ||       |  |||||||| || || || || || || |||||||| ||||| ||  |||||||||||||||| || ||||| ||||||||||| |
gtttgtctcaatttctcatgcaataattatccctccctgac--ttat-tgttactgacataggatgtg------gaatgatagGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------gtta-gtggagttttctttcata---tagcttatttcttaccaaaagttatatatt----------tttaagctactgagtca-----ctcttggt-------tgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
                                              ||||  |||  ||||   | | |   | | ||   |   |  ||| |   ||  ||          ||||   || | | |||     ||||||||       |  ||||| || || |||||||||||||||||||| ||||| ||  ||||||||||||||||||| || || ||||| |||||||
gtaagcgatcttcgtctctttatgattcaccacttatgtaaccttagttatatggtatttttcgtgacaatctggtttgcgtgagagtaaacgacgtaatttgggcaccgtgtttagaatattaactcaaatggctcttggtgacggtgttctagGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------gtta-gtg-gagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
                                                                     ||  ||| ||||   |  |   |  |    |||  |  || ||||| ||  | | | | |   ||   |  |  ||      |||| || |||||||| |||||||| ||||| ||||| ||  ||||||||||||||||||| || |||||||| ||||| |
gtgagtagcctcctacttgtggtcctctactgagtctatcttggatgctacttttgatgttgatctgaattgcgtgagagtgaacgatgtcaatgggcgttttgtctcagaagttgtaattatcttatcatttgtagcggtggtg-----cagGTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
                      | | |   ||| |   | |||||| |||  |     ||  ||      ||||| ||  ||||| || || |||||||||||||| ||||| ||||| ||||||||||||||||| || || |||||||| || ||||| |
--------------------gttggttgtcttcgtttgacaagttacatacat---gacttttg------tcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 9
gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
                      | | |  |||| |   | |||||| |||  |     ||  ||      ||||| ||  ||||| || || |||||||||||||| ||||| ||||| ||||||||||||||||| || || |||||||| || ||||| |
--------------------gttggttgttttcgtttgacaagttacatacat---gactcttg------tcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG

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|124712319|gb|EH803721.1|EH803721
EST:     TATACCAGTTGATGAGCGAATGTCGTGTTATTGATGGAAATGGAAAGCTG                         GTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGA
genomic: TATACCAGTTGATGAGCGAATG-CGTGTTATTGATGGAAATGGAAAGCTGgttagtggag ... tggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGA
EST: gi|125001682|gb|EL073951.1|EL073951
EST:     CAGTTGATGAGCGAATGCGTGTTATTGATGGAAATGGAAAGCTG                         GTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATG
genomic: CAGTTGATGAGCGAATGCGTGTTATTGATGGAAATGGAAAGCTGgttagtggag ... tggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG
  ttcttac  putative branch site (score: 2)
                                      tcactctt  putative PPT
     ttaccaaaagttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA