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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G55490.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 9
----------------------------gtaaactaaaa--actatttaagtt--tcctttgtctgatta-------agatgtg-tttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
                            || | ||  |     | |||   ||  | |||||| ||   |       ||||||| ||     | |  |||   ||| |  || | || |  | | |||| ||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| || ||||| || |||
gtataataagaaatggacaaaatgccatgttatctgtatctgttctttttcttggttctttgtttggaaagatagatagatgtggttatgtgggtcgtaatccaagtt--ttgt-tacttttgatagGTGGGAGCACAAACAGAGACCGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCTACCAAG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 8
---------------------gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagtta----agctcgt-tatg-tattggttaa-agGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
                     | ||  |   |  | || ||  ||| |||    |||| |    |||| |||  ||  |   | |    |  || | ||||   ||| || | |||| ||||||||||| || || ||||| ||||||||||||||||||||||| ||||| || |||||||| |||
gtaatgtgaagtccacgggtcgcaatgtgttatttgttcaatgttcttttcatcgattcaa---tgttgcaggtatggtggataaccataattcatgtatggcgttgcttgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCAACTAAG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 3
----------gtaaactaaaaactatttaagtttcctttgtctga------------ttaagatgtgtttcagagatattaagt-----taag-ctcgttatgtattggttaa-agGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
          ||| ||  |  || ||||  || |  |||||  ||            | |     ||||  |  |||  |   |     |||| |   |   || |||  | | |||| ||||||||||| || || ||||| |||||||||||||| |||||||| ||||| || |||||||| |||
gtattgtgaagtacacagatcacaatttttgtgttatttgttcgacgttctttccattgattgaatgttgtaaggatggtggataactgtaagtcatatctggtgttgcctgacagGTGGGAGCACAAACAGAAACTGAACTAAAAGAGAAGAAGTTAAGAGTTGAGGATGCCCTAAATGCAACCAAG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 8
gtaaactaaaaactatttaagtttcctt-tgtctgattaagatgtgtttcagag-atattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
||||    | |   | | || | |  |  | | | | |  | |    | ||  | |||| || ||  |    || |        || ||||||| ||||||||||||||||| ||||| || ||||| |||||||||||||| ||||||||||| ||||||
gtaac---agactcactgaaatgtggtaatatattagtttggtactctgcaaggtatatcaacttggggcaatttttgtacatatatagGTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtt-tcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
       | | |||   | |  |     | | | | |  | |  |   |  |  |||| || ||  ||   || ||||   ||   ||||||| |||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||| ||||||
----gtaacagactcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgt-gtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagt-taagctcgttatgtattgg----ttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
||||| |   |  || |  ||||    || | | | | |  |     |   || |  | ||| |    |  ||||  ||||     || |||||||||||||||||||||||||| || ||||| |||||  ||||||| ||||| ||||| |||||||| |||
gtaaattcttagttagtccagttaaaatt-tataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 8
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
                 |||||||  ||||    |||         || ||    |     ||||  ||  | |  ||||    |||||||| |||||||||||||||||| | ||||| |||||||| ||||| ||||||||| | ||||| || |||
----------------gtaagtttattttgcagtatt---------tttagcagcacatctttaacttctctgtaaattg----aagGTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAG

upper sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 8
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
                 |||||||  ||||    |||         || ||    |    |||||  |   | |  ||||    |||||||| |||||||||||||||||||| ||||| |||||||| ||||| ||||||||| | |||||||| |||
----------------gtaagtttattttgcagtatt---------tttagcagcacatcgttaacttttctgtaaattg----aagGTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAG

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|125224063|gb|EL238148.1|EL238148
EST:     AGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAA
genomic: AGTTGCTGTGATTCAGgtaaactaaa ... ttggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAA
EST: gi|47832210|gb|CK121894.1|CK121894
EST:     AACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAG                         GTTGGAGCACAAACTGAGACAGAACTCAA
genomic: AACTCAATGAGAGAATTGCAAAGCTCTCTGGTGGAGTTGCTGTGATTCAGgtaaactaaa ... ttggttaaagGTTGGAGCACAAACTGAGACAGAACTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG
 gtctgat  putative branch site (score: 4)
                   agatattaagttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtttcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG