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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattgaatttttggcttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT

Basic information

species Arabidopsis thaliana
transcript AT4G13170.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G02790.1 (Glycine max), 3'ss of exon 1
tctttgtgaagattcagt-gatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattgaatttttggcttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
 |   | || |      | |||  || |   ||| |    |  ||      |||    ||      ||   ||||  |||   | | || |||  ||| || ||||| ||||||||||| |||||||| |  ||||| |||||||| |||||||||| ||| |||||||| ||||| || |||||||  ||||||||||||
-cagggagagggagagatagataaagagaaataagaggtgttgagagggagtttagaatttgtgggtgtctaaatataatcactcgtttgtgtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G13670.1 (Glycine max), 3'ss of exon 1
---tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtct--ttctttttttttgagttttggtgaaatt--gaatttttggcttttgtgg-----ttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
   | | ||| |   ||   |  | |    |  |   |   || ||  ||  |||  ||| ||  |   ||||  |  ||  |  ||||   || |||| |     ||| || ||||| ||||||||||| |||||||| |  ||||| |||||||| |||||||||| ||| |||||||| ||||| || |||||||  ||||||||||||
gtctgtctgtcactttttgttattattatttcatctcatgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 1
-----tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattgaatttttggcttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
     |  |||   |  ||  || ||      | |   | ||| |    |   | |  ||| ||| |    ||  |  ||     |     || |||   || || ||||| ||||||||||| |||||||| |  || || || ||||| |||||||||| ||||||||| || ||||| || |||||||| ||||||||||||
gagattgattgaagaatttttgt-atactatatctatctgaaggtaggatggatttaatttgttgtgggaagggaaggtt----ctgaaatttctgtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G46860.1 (Glycine max), 3'ss of exon 1
tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattga-atttttggcttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
  || | |   ||    | |||    |   | || ||  || | |     ||  |  |   ||| |||  |  ||   |     |   |||||| |||||||||||| ||||||||||| ||||| || |  ||||| ||||| || |||||||| | |||||| || || |||||||| |||||||  ||||| ||||||
atttggggctaatgtgtttatg-gttgacattatgaacttgtaatgaagattactggtgttgttgtggaaagttttctaagacggatgtttgtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G46850.1 (Glycine max), 3'ss of exon 1
tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattgaatttttggct-tttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
  | | ||  | |   ||| | ||  |||   || | ||    ||  |     ||  | | ||| |||  |  ||        || | ||||||  ||||||||||| ||||||||||| ||||| || |  ||||| ||||| ||  ||||||| |  ||||| || || |||||||| |||||||  ||||| ||||||
attatatggggctaatgtgtt-tatggttggcattatgaacttgtaatgaagattactggtgttgtggaaagttttctgagaaggatgtttgtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
-tctttgtgaagattcagtgatgtagcgtt-ttaataaagatgaagtctttctttttttttgagttttggtgaaattgaatttttggcttt-tgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
 | || |||    | |  |    |  | |  |||   |  ||  ||   ||  |||       |||||     ||||   ||||||| ||| | |  ||| ||||||||||| ||||||||||||||||| || || || ||||| || ||||||| || |||||||||||| || || || || ||||| ||||| ||||| 
attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatt---tttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0029g00020.t01 (Vitis vinifera), 3'ss of exon 1
------------------------tctttgtgaag-----attcagtgatgtagcgttttaataaagatgaa-gtctttctttttttttga-gttttggtgaaat---tgaatttttgg-----cttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
                        | ||| || |      ||||   ||      |||||  | |  ||     | | | | ||  | ||| | |||| |  |     | || |          ||||   | ||| ||||||||||| |||||||| |||||||| || || || |||||  | ||||||| ||  ||||| || |||||||| || || ||||| ||||| ||||||
gtgagcttgacttatcattttatatttttctgcattttctattccacgaaacgaagtttttttcattattttcatttatttattaatatgatgctttgattgagccaataaaatcccaaaatctctttctggtttgtagGATGATTCCTCACAAGACTAAGCGTGGAGCCGCAGCGCTTGCCAGATTGAAGGCTTACGAGGGGATTCCACCTCCATATGATAAGATGAAGAGGATGGTT

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S165_40V6.1 (Physcomitrella patens), 3'ss of exon 2
tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattgaattt--ttggcttttgtg-----gttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
         || || || |        ||  |   ||  |    |  |||        |   | |||  |   |   |      ||  | || |      |||| || ||||| || |||||||||||| | ||||||||||| ||||  ||||||||||  ||||| ||| ||||  | || || |||||||| || |||||||||
-------atagcttgagagtcagtcttttccatccaacttctgattcttccacccaaatagctattgaagggctgagacccgactgattcttataaatctgttgtagAATGATCCCTCACAAGACCAAGAGGGGTGCTGCTGCTCTTGAGCGCTTGAAGGCCTTTGAAGGAGTCCCTGCACCGTATGACAAGATGAAAAGAATGGTT

upper sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S174_48V6.1 (Physcomitrella patens), 3'ss of exon 2
tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttcttttttttt-----gagttttggtgaaattgaatttttggcttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
|   |   |   | || |  | |   |||  ||  ||  | ||   ||| |||| ||       ||  |||  |   |   |||| |     ||||     |||| ||||| || |||||||| ||| | || |||||||| ||||  ||||||||||  || |||||  ||||| ||||||||||||| || ||||| ||||| 
tgaattacagattccattcttatcaggttcaaaccaaagttaaccatttattttgttaaaataagaactttcatctgaacaaattatgtcactttg-----gcagAATGATCCCGCACAAGACAAAGAGGGGAGCTGCTGCTCTTGAGCGCTTGAAGGCATTCGAGGGTGTCCCAGCTCCTTACGACAAAATGAAGAGGATGGTC

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|116477676|gb|EG520268.1|EG520268
EST:     CCTATTCACTTTCGTGCTCCTTCCAAGATCTTCTGGCGCACTGTTCGCGG                         GATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAA
genomic: CCTATTCACTTTCGTGCTCCTTCCAAGATCTTCTGGCGCACTGTTCGCGGgttcgttcgt ... gtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAA
EST: gi|116477675|gb|EG520267.1|EG520267
EST:     CCTATTCACTTTCGTGCTCCTTCCAAGATCTTCTGGCGCACTGTTCGCGG                         GATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAA
genomic: CCTATTCACTTTCGTGCTCCTTCCAAGATCTTCTGGCGCACTGTTCGCGGgttcgttcgt ... gtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAA
EST: gi|163992045|gb|ES200870.1|ES200870
EST:     AAGATCTTCTGGCGCACTGTTCGCGG                         GATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAA
genomic: AAGATCTTCTGGCGCACTGTTCGCGGgttcgttcgt ... gtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAA
EST: gi|124903333|gb|EH977413.1|EH977413
EST:     CTTTCGTGCTCCTTCCAAGATCTTCTGGCGCACTGTTCGCGG                         GATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGA
genomic: CTTTCGTGCTCCTTCCAAGATCTTCTGGCGCACTGTTCGCGGgttcgttcgt ... gtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctttttttttgagttttggtgaaattgaatttttggcttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT
                                        cttttgt  CT-rich tract
     tttttttttgagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattgaatttttggcttttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - ataaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttttgg