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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttacttaaagattttgataggtctatataggttctctctcttgttaaccacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG

Basic information

species Arabidopsis thaliana
transcript AT2G46230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 4
-----------------------gtgagttacttaaagattttgataggtctatataggttctctctcttgttaaccacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
                       | |  | |  ||    ||||   |  | |  | | |    |    ||| | || |  | ||     |  || | ||||||||| || ||||||||||||||||| ||||| ||| | || ||| | || || ||||||||||||||  | ||
tataatatggaatggaacgagtagggtttaagctatcctttttagcatattttgaaatgcatacggctttgctgacaaagtctacca--tcttgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G017761_T01 (Zea mays), 3'ss of exon 4
----------------------gtgagttact-taaagattttgataggtctatataggttctctctcttgttaaccacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
                       ||  || |  | |   ||||| |      | |||     |   | |  ||   || || | ||   || |  | |||||| || || ||||||||||| ||||| ||||||||| | || ||| | || |||||||||||||| ||  | ||
gtaagcatttaactctgttatcttgcattcccattatctttttggtgaactgagatacccctttaatatcttt--tcaactctgatgccttgt--tatgaagGTACCCCATGTATCACGGACTGTGTTATGGCTGAGCTTGAAAAGCTGGGGCAGAAGTATCGTGTGGCCTTGAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G016330_T03 (Zea mays), 3'ss of exon 4
----------------------gtgagttact-taaagattttgataggtctatataggttctctctcttgttaaccacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
                       ||  || |  | |   ||||| |      | |||     |   | |  ||   || || | ||   || |  | |||||| || || ||||||||||| ||||| ||||||||| | || ||| | || |||||||||||||| ||  | ||
gtaagcatttaactctgttatcttgcattcccattatctttttggtgaactgagatacccctttaatatcttt--tcaactctgatgccttgt--tatgaagGTACCCCATGTATCACGGACTGTGTTATGGCTGAGCTTGAAAAGATGGGGCAGAAGTATCGTGTGGCCTTGAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 5
-----------------gtgagttacttaaagattttgataggtctatataggttct-ctctcttgttaacc---acctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
                  || |  | |   |   | |  | |    | | |     |  ||| || ||| |      || |   | |||  | |||  |||||| |||||||| ||||| ||||| ||||| ||  | ||||||||||| || || |||||||||||||||||
agaagctcgtctttgtaatgtggcattggcattgtatatttgaatcaaacatcccatattctattattacctttgttctattgatattttggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAGTTAGGCCAAAAATATCGTGTAGCTCTAAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G41500.1 (Glycine max), 3'ss of exon 3
-------------gtgagttacttaaagattttgataggtc--tatataggttctctctcttgttaac------cacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
             |    | |  |  | ||||  |     |     | ||   |  ||| || ||| |      |  || |   |  ||  | |||  |||||| ||||||||||| || ||||| ||||| ||  | ||||||||||| || || |||||||||||||||||
ttgccaggattaagaagatgatctttatatttgaaccaaacatctcacagtcacattctattcttacctttgttcttctattcatactttggattttcagGCACCCCTTGTATCACAGACTGTGTGATGGCAGAACTTGAGAAGTTAGGCCAAAAATATCGTGTAGCTCTAAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 5
-------------gtgagttacttaaagattttgataggtcta--tataggttctctctcttgtta--accac----ctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
             |   ||   |  ||  |     | |   ||   | |  | |  | |  | |||  ||| |    || |   | |||  | |||  |||||| |||||||| ||||| ||||| ||||| ||  | ||||| ||||| || || |||||||||||||||||
tctagattaagaagcttgtctttgtaatgtggcattggcattaatcaaacatcccatattctattattacctctgttctattgatattttggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gtgagttacttaaagattttgataggtctatataggttctctctcttgttaaccacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
                         |  || ||  |  |  ||  |    |||||   ||   | ||||  |  |  |||   ||  |||    ||| |||||||||||||||||||||||||||| ||||| ||| | ||||||||||||||||| || || || ||||| ||
taaattttttatcttatcaatctgaaagtatttttatgtgatgggattcttatattattttgttgtctttgttgcttccttctatc-ttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG

upper sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S153_101V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------------------gtgagttacttaa-agattttgatag-gtctatataggttctctctcttgtt---------aaccacctg--taattgttt--ctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
                                                                     | || ||  |  | |||  || |  |  || |  | | |||| | || ||||          |  || ||  |||   |||   |||  |  ||| || |||||||||||||||||||| ||||| || |||||||| || |||||||||||||| || ||| ||||
gtaagtagcttgctttcgccagcggtttcattgttgtttttctgaatacctagtgtttattcgttgctagagaattggtccatagaagtttacggtatcaaggttgcttctgtatcctgtttgattgggcgagtacatgattaacgatttgtttggcctacagGTACACCTTGTATCACGGATTGTGTGATGGCCGAATTAGAGAAATTGGGTCAGAAGTATCGCGTCGCTTTAAG

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|86051132|gb|DR346887.1|DR346887
EST:     ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATT                         GCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC
genomic: ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATTgtgagttact ... tggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC
EST: gi|86051135|gb|DR346890.1|DR346890
EST:     ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATT                         GCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC
genomic: ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATTgtgagttact ... tggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC
EST: gi|86051133|gb|DR346888.1|DR346888
EST:     ATCGATCTTGAGAAGGGA-TGAGAGACTGTCTGTACGCAAATT                         GCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAG
genomic: ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATTgtgagttact ... tggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAG
EST: gi|86051134|gb|DR346889.1|DR346889
EST:     ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATT                         GCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC
genomic: ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATTgtgagttact ... tggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC
EST: gi|86080730|gb|DR376487.1|DR376487
EST:     WTCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATT                         GCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC
genomic: ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATTgtgagttact ... tggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC
EST: gi|47828370|gb|CK118054.1|CK118054
EST:     ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATT                         GCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC
genomic: ATCGATCTTGAGAAGGGAATGAGAGACTGTCTGTACGCAAATTgtgagttact ... tggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtctatataggttctctctcttgttaaccacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
                      tgttaac  putative branch site (score: 2)
                                      ttgtttct  putative PPT
                                   taattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttacttaaagattttgataggtctatataggttctctctcttgttaaccacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT