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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttggcatatctttctttgaattcagagaagacttggtgctatctgaactaagcaagtgtaaatggtacagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC

Basic information

species Arabidopsis thaliana
transcript AT2G05990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
---------------------gttggttggcatatctttctttg---aattcagagaagacttggtgctatctgaactaagcaagtgtaaatggt-acagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
                       ||   |  || | |    | |   ||  || || | | ||  |  |       ||||     || |  |  | ||||| |||||||| || ||||||||  | |||||||||||||||||||| ||||| ||||||||| |||||||||| ||||| || || ||  | ||||| ||
aagtgctactaacttgtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 2
---------------------------gttggttggcatatctttctttgaattcagagaagacttggtgctatctgaactaagcaagtgtaaatggtacagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
                           |       ||||||   |  |  || ||       | ||| ||| |        | |   || | |    | |||| ||||| || |||||||||||  | |||||||| ||||||||||| ||||| || |||||  |||||||||||||||| ||||||||  | ||||| ||
gagagatttttttttcaaaaaaacagagaactcgagcatattagtagtacaaatccttctcaa-ttgctgccactcttctaatgtttgtatgatctct-cagGTAAAAGGGCGTTCATTGCTGGAGTTGCTGATGACAATGGCTATGGCTGGGCAATTGCAAAGGCTCTTGCTGCTGCTGGTGCTGAAATTCTTGTTGGTAC

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G079256_T01 (Zea mays), 3'ss of exon 2
---------------------gttggttggcatatctttctttgaattcaga---gaagacttggtgctatctga-actaagcaagtgtaaatggtacagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
                      ||   |     ||||    |      || |    |  |||    | | || || |  ||  |  |   ||   | |||| |||||||| || || |||||  | |||||||||||||| ||||||||||| || || ||  |||||||||||||||| ||||| ||  | ||||| ||
gtacatgatctggcaattttttttatctatgggatctgaactaatgcacatattcaataactgcaagttttcagacatcaattatcttgcaagttttcagGTAAAAGAGCATTTATAGCTGGAGTTGCTGATGATAATGGTTATGGTTGGGCAATTGCTAAGGCTCTTGCTGCTGCTGGTGCTGAGATTCTTGTTGGTAC

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 2
--gttggttggcatatctttctt------tgaattcagagaaga---cttggtgctatctga---actaa--gcaagtgtaaatgg---------tacagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
  |||| |||| |    ||  |       ||||  || | |||    |||  ||  |  |      ||||  | |||| | |||           |  ||| ||||| || |||||||||||  | |||||||||||||||||||| ||||| || || ||  | |||||||| ||||| ||||||||  | || || ||
ttgttgtttggtagcctttattcaaagaatgaaaacataaaaggaacctttttgtcagtttgctctctaactgtaagttttaatcactacaattttttagGTAAAAGGGCATTCATTGCTGGAGTTGCTGATGATAATGGCTATGGATGGGCAATTGCGAAGGCACTTGCTGCGGCTGGTGCTGAAATTCTTGTGGGTAC

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 2
------------------gttggttggcatatctttctt--tgaattcagagaagacttggt--gctatctgaactaagcaagtgt-aaatg--gtacagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
                  |     ||  |  | ||||||  |   ||      |   ||| |  | | |   |    |   | ||| |  ||  || |||| ||||| ||||||||||||||| | |||||||| ||||| ||||| ||||| ||||||||||||||||| || || |||||||||||  | || || ||
tctcataaatttgttattgccaagtgtaacttttttcttactaccttttttatatctttgattcgttgtggcattccactgaatgttatgtgatgtgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTTGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
--------------gttggttggcatatctttctttgaa-------ttcagagaagacttggt--gctatctgaactaagcaagtgtaaatggtac--agGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
               |||    |  || |||| ||   |       ||      |   ||| |  | | |   |    |   | ||||  || | |  ||| ||||| ||||||||||||||| | |||||||| ||||| ||||| ||||| |||||||||||||| || || || |||||||||||  | || || ||
ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
----------gttggttggcatatctttctttgaattcagagaagact-tggtgctatctga-actaagca-------agtgtaaatggta-------cagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
           ||| ||||  |||||||   |  ||   ||     || || |    | ||| |  ||  |       | || |||| | |        ||| ||||| ||||| ||||||||| | |||||||| ||||| ||||| ||||| || ||||||||||||||||| || |||||||||||  | ||||| ||
aattttgtaatttgattggt-tatcttttcatagatatggattttgctatgatagagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 2
---------gttggttggca-tatc-tttctttga-attcag--agaagacttggtgctatctg----aactaagcaagtgtaaatggta-------cagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
          ||  |||    || |  || ||||| | |  |  | |  |  ||   | ||||      ||||| | |   ||    |||       |||| || || || || ||||| ||| |||||||||||||||| ||||||||||| ||||||||||| ||||||||||| |||||||||||  |  |||| ||
aagaaccaaattaattgcttctaccacttgtttgatacttggtcacacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC

upper sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
--------------------gttggttggcatatctttctttga--attcagagaagacttggt-gctatctgaactaagcaagtgtaaatggtac----agGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
                    | |  |||  |  |   |  ||||  |  || | || |   | |  |    | ||||||  || ||  | || ||     ||| || ||||| || ||||||||| | |||||||| ||||| ||||||||||| ||||| ||||||||||| ||||| || ||||||||  | ||||| ||
gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaaaaataagattacctcttcaactaa--aactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC

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|47831556|gb|CK121240.1|CK121240
EST:     TGAATCCAGTGAAAACAAGGCTCCTTCAGGGCTTCCAATTGATTTGAGAG                         GGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGG
genomic: TGAATCCAGTGAAAACAAGGCTCCTTCAGGGCTTCCAATTGATTTGAGAGgttggttggc ... aatggtacagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGG
EST: gi|125110940|gb|EL162658.1|EL162658
EST:     TGAATCCAGTGAAAACAAGGCTCCTTCAGGGCTTCCAATTGATTTGAGAG                         GGAAAAGAGCTTTCATTG
genomic: TGAATCCAGTGAAAACAAGGCTCCTTCAGGGCTTCCAATTGATTTGAGAGgttggttggc ... aatggtacagGGAAAAGAGCTTTCATTG
EST: gi|124999253|gb|EL071522.1|EL071522
EST:     GGGCTTCCAATTGATTTGAGAG                         GGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGG
genomic: GGGCTTCCAATTGATTTGAGAGgttggttggc ... aatggtacagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaattcagagaagacttggtgctatctgaactaagcaagtgtaaatggtacagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC
                                         tgtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttggcatatctttctttgaattcagagaagacttggtgctatctgaactaagcaagtgtaaatggtacagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA