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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttcttgaagatccatgtgaccagaatctttaatatttgctgattcagcatttgacttattatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttcttgaagatccatgtgaccagaatctttaatatttgctgattcagcatttgacttattatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
                                | || |  | | |||  |||  ||| | || ||   |||   | |      ||| || | ||| ||||  || | ||  ||| | ||| | ||  | | ||    || | |||||| ||||||| || |||||||| ||||| ||||| |||||||| ||| |||||||||| |||||||| || || ||||||||||| || |||
--------------------------------aattctgcaacataga-gaatctagatattattctcgatagttttattggcaatattaactatatgcttgttga-caagtgagtgattgtttaactttgta----gGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggc-gaaagtagttgtt-cttgaagatccatgtgaccagaatct--ttaatatttgctgattcagcatt-tgactt---attatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
       | || | | |    | | ||||   || | |  || | |||| ||  ||   | |  | |   | |   |||  |     |||  ||| |        | |||  ||| ||| ||   |||||  |||||    || |||   | |||| |||||||||| || ||||| ||||| ||||| || ||||| ||| ||||||| || |||||||| || || ||||| ||||||||||||
-----gttggctgctaa---cgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccat-agGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 5
-----------gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttcttgaagatccatgtgaccagaatctttaatatttgctgattcagcatttgacttattatctacttgtataat-tagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
           | |||  || |  ||  |||||||    ||     || || | || |||  |   |   |     ||| |   |  |  |   ||| |  |    || ||| |||   |  | | || |  |  | ||| || ||  |||||||| ||  ||||||| || || ||||||||||| || ||||||||||||||||||||||||||||| ||||| || |||||||||||||||||||| 
gttctatgaagggaaaaattacctttccatctgttcatctgttgtataatt-tgtttggcatacacatgaga----gaaaaattacctttcataaatatgcagctgttcctgtttctttaact-atttctgtttaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 3
gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttcttgaagatccatgtgaccagaatctttaatatttgctgattcagcatttgacttattatctacttgtataat-tagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
                               || || |||  | ||  |   ||            || |   |  |  |   ||| |  ||  ||| ||| |||   |  |    | |  || | ||| || ||  |||||||| ||  ||||||| || || ||||||||||| || ||||||||||||||||||||||||||||| ||||| || |||||||||||||||||||| 
------------------------------taatttgtttggcatatacatgagaga---------aaaaattacctttcataaatatacaacttttcctgtttccttaactattgtttgttcaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 5
-----------gtaaaccttgcagttg----aatctgttatgttgaaacttatttatcttaggcgaaagta-----gttgttcttgaagatccatgtgaccagaatc---ttta-----atatttgctgattcagcat-ttgacttattatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
            | ||  ||     ||    ||||| |    | | ||  | || || ||      | ||      |||| | || ||  | |||   |  | | |    ||||     ||   |  |||| | |  | || | |  ||   ||    |  |   ||||| || || || |||||  | || ||||| ||||| || ||||||||||||||||||||||| ||||| ||||| || |||||||||||||||||||||
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 5
-----------gtaaaccttgcagttg----aatctg----ttatgttgaaacttatttatcttaggcgaaagta----gttgttcttgaagatccatgtgaccagaatct------ttaatatttgc--tgattcagcatttg-acttattatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
            | ||  ||     ||    |||||     ||||   ||| ||| | |   | |   ||   |     |||| | || ||  | |||   |  | | |        | ||||| | |  |||| | |  | || | |  ||   ||    |  |   ||||| || || || |||||  | || ||||| ||||| || ||||||||||||||||| ||||||||||| ||||| || ||||||||||||||||| |||
gtttgtcttagctgaattttatttctggtgtaatctaggtcttattaggaagcttttgttaatgaaatgatgttttcatgttgctttttaatttacatacaaggacatttccatttatgaatatgtacagtgatcctgtttgtgcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTAAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACTGCT

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 5
gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttct-tgaagatcc--atgtgaccagaatctttaatatttgctgattcagcatttgactt-att--atctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
                                         | |||     |   |  |  | | |||  |||   ||  || | || |||||| || |   |||||     ||| |||| |||  |||||  ||   ||| ||| |||| ||  ||||| | || || ||||| ||||| ||||||||||||||||||||||||||||| |||||||| || |||||||| |||||||| || 
-----------------------------------------tgttaaattcagaaatctactatgtgatcatcagaataagaactgactctttagtaatcagtgatt---tgtttaactttatttgatctatctgacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGGTGATTTGAAATGCAAGGAGGTTCCCACAAGTTTTGGATTTGATACTGCA

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|164090140|gb|EL981229.1|EL981229
EST:     GGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAG                         GAGTAAGAACTTGAAAACCC
genomic: GGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCC
EST: gi|164046115|gb|ES162500.1|ES162500
EST:     CCAATGCTTGCCTTCTTGCTGAAAACTTCAG                         GAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
genomic: CCAATGCTTGCCTTCTTGCTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
EST: gi|125020009|gb|EL092278.1|EL092278
EST:     CTGAAAACTTCAG                         GAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
genomic: CTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
EST: gi|124794408|gb|EH884087.1|EH884087
EST:     AACACCAATGCTTGCCTTCTTGCTGAAAACTTCAG                         GAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
genomic: AACACCAATGCTTGCCTTCTTGCTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
EST: gi|164231176|gb|ES041098.1|ES041098
EST:     GCCTTCTTGCTGAAAACTTCAG                         GAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
genomic: GCCTTCTTGCTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
EST: gi|125065356|gb|EL132616.1|EL132616
EST:     GGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAG                         GAGTAAGAACTTGAAAACCCGAGTCATTGGGTG
genomic: GGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTG
EST: gi|164215770|gb|ES019641.1|ES019641
EST:     GCCTTCTTGCTGAAAACTTCAG                         GAGTAAGAACTTG-AAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
genomic: GCCTTCTTGCTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
EST: gi|164196437|gb|ES095419.1|ES095419
EST:     GGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAG                         GAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCA
genomic: GGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCA
EST: gi|116438055|gb|EG480647.1|EG480647
EST:     GGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAG                         GAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCC
genomic: GGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCC
EST: gi|116438054|gb|EG480646.1|EG480646
EST:     TCTTGCTGAAAACTTCAG                         GAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG
genomic: TCTTGCTGAAAACTTCAGgtaaaccttg ... gtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctttaatatttgctgattcagcatttgacttattatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT
                                ttattatctacttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttcttgaagatccatgtgaccagaatctttaatatttgctgattcagcatttgacttattatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG