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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatcaatcaggttctactacttcagtttcctgagaccataaccatatatctcaaaatcttgtatcctgatgagttttcgtaaacaagactacgcgcagctgcatcgttaacatgaatatgcgagcatcgtcttagcttagaagaactgtataatcggaaatacttttctcatttcttgcctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA

Basic information

species Arabidopsis thaliana
transcript AT3G48420.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G36600.1 (Glycine max), 3'ss of exon 4
gtatgatcaatcaggttctactacttcagtttcctgagaccataaccatatatctcaaaatcttgtatcctgatgagttttcgtaaacaagactacgcgcagctgcatcgttaacatgaatatgcgagcatcgtcttagcttagaagaactgtataatcggaaatacttttctcatttcttgcctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA
                                                                                      |  ||| ||       ||| ||   | | ||     ||         ||     |||       | | | ||   |  | |    || | || |    |||||| |||| ||||| ||||| |||| |||||| ||||| ||  ||||||| |||||||||||||| ||||||||||| || |||   || || |||||||| 
--------------------------------------------------------------------------------------attagattaattatcactgaatgaatcatattgcactggtgattggatccacattta-------tttgttatttcatcttcagacctaagttgtgagttgattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT

upper sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G18320.1 (Glycine max), 3'ss of exon 5
gtatgatcaatcaggttctactacttcagtttcctgagaccataaccatatatctcaaaatcttgtatcctgatgagttttcgtaaacaagactacgcgcagctgcatcgttaacatgaatatgcgagcatcgtcttagcttagaagaactgtataatcggaaatacttttctcatttcttgcctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA
                                                                                      |  ||| ||       ||  ||   | | ||     |||     |  | | | |    || |  | | |  |     || |    || | || |    | |||| |||| ||||| ||||| |||| |||||| ||||| ||  ||||||| |||||||||||||| || |||||||| || |||   || || |||||||||
------------------------------------------------------------------------------------ttattagattaattatcacttaatgaatcatat-----tgcactggtgatttgatc----aacatttatttgttatttcattcagacctaagttatgagttcattttagGTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCCGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCA

upper sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 3'ss of exon 4
gtatgatcaatcaggttctactacttcagtttcctgagaccataaccatatatctcaaaatcttgtatcctgatgagttttcgtaaacaagactacgcgcagctgcatcgttaacatgaatatgcgagc-atcgtcttagcttagaagaactgtataatcggaaatacttttctcatttcttgcctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA
                                                                                               |  ||     ||| ||     |   |  ||||   ||  | || | ||          |          |||  |   | || | |      ||  ||||| ||||| ||||||||||||||||| || || || |||||||| |||||||||||||| ||||| ||||| || ||   ||| || |||||||||
----------------------------------------------------------------------------------------------tcttgctttgtcattgtctgatttccttggcgaattatgatattggttttctgatctaattctcattttgataactgaattatatgtgctaatatcccagGTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATCAAGATATTTGCAGGCGACGTGGTTCCTCGAAAAAAGCCTGATCCA

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|86078346|gb|DR374103.1|DR374103
EST:     TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCG                         GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATC
genomic: TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCGgtatgatcaa ... ctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATC
EST: gi|124918778|gb|EH992586.1|EH992586
EST:     CAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCG                         GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATC
genomic: CAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCGgtatgatcaa ... ctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATC
EST: gi|124866887|gb|EH951324.1|EH951324
EST:     AGCTGTGTGCAGTACTTCAAATGAGAAGGCG                         GTTTCTGCTATAGTTT
genomic: AGCTGTGTGCAGTACTTCAAATGAGAAGGCGgtatgatcaa ... ctgatttcagGTTTCTGCTATAGTTT
EST: gi|125171797|gb|EL194443.1|EL194443
EST:     TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCG                         GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAA
genomic: TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCGgtatgatcaa ... ctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAA
EST: gi|125141483|gb|EL178984.1|EL178984
EST:     GCTGTGTGCAGTACTTCAAATGAGAAGGCG                         GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATC
genomic: GCTGTGTGCAGTACTTCAAATGAGAAGGCGgtatgatcaa ... ctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATC
EST: gi|47832151|gb|CK121835.1|CK121835
EST:     TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCG                         GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATC
genomic: TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCGgtatgatcaa ... ctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATC
EST: gi|124834524|gb|EH918963.1|EH918963
EST:     TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCG                         GTTTCTGCTATAGTTTCATGACTTGCTTGGACCAGAACGAGCAGAGAA
genomic: TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCGgtatgatcaa ... ctgatttcagGTTTCTGCTATAGTTTCATG-CTTGCTTGGACCAGAACGAGCAGAGAA
EST: gi|125075727|gb|EL139160.1|EL139160
EST:     TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCG                         GTTTCTGCTATAGTTTCATG
genomic: TAACAAACGGAGTCAAAGTAGCTGTGTGCAGTACTTCAAATGAGAAGGCGgtatgatcaa ... ctgatttcagGTTTCTGCTATAGTTTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttagaagaactgtataatcggaaatacttttctcatttcttgcctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA
                                           gcctgat  putative branch site (score: 4)
                          tacttttctcatttct  CT-rich tract
                       aaatactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatcaatcaggttctactacttcagtttcctgagaccataaccatatatctcaaaatcttgtatcctgatgagttttcgtaaacaagactacgcgcagctgcatcgttaacatgaatatgcgagcatcgtcttagcttagaagaactgtataatcggaaatacttttctcatttcttgcctgatttcagGTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA