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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttacttaataagtgccctgaaacttagtctttttgttctctttgttagttgacattgctaaggctaccttgtagttactttgaggaagtcactttgttttttacctcttacctattttgtgtgttggacag

Basic information

species Arabidopsis thaliana
transcript AT5G23300.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G43220.1 (Glycine max), 5'ss of exon 2
GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttacttaa-----taagtgccctgaa-acttagtctttttgttctctttgt-tagttgacattgctaaggctaccttgtagttactttgaggaagtcactttgttttttacctcttacctattttgtgtgttggacag
|||||| | ||||||||||| ||||| |||||    |||||||| ||||||||||| |||||||  |||||||| || ||||||||||| | ||       | | ||   |    | || || ||  |  |||  || | || ||||  |     ||  |  |||||  ||  | |||||||                                            
GGAAGGTTGTTGACAGGAGCCACCATAGGTCTACTTATAGCTGGTGGAGCTTATGTGAGTACTGTGGATGAAGCTACTTTCTGgtacttcatttgggagtttgaatgttgtatgcattttgttttgctcctctaattctgtatttgatgtgttatagtattacttgtttttcttgtgaggaaa-------------------------------------------

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G23670.1 (Glycine max), 5'ss of exon 2
GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttacttaa-----taagtgccctgaaacttagtctttttgttctctttgttagttgacattgctaaggctaccttgtagttactttgaggaagtcactttgttttttacctcttacctattttgtgtgttggacag
|||||| | ||||| ||||| ||||| |||||    |||||||| ||||||||||| |||||||  |||||||| || ||||||||||| | ||       | | ||   |     || |  ||||  |    ||    | ||||  | | ||  |     | ||  ||| | | ||||||  |                                        
GGAAGGTTGTTGACGGGAGCCACCATAGGTCTACTTATAGCTGGTGGAGCTTATGTGAGTACTGTGGATGAAGCTACTTTCTGgtacttcatttgggagtttgaatgttgtatgcatttggtttttcctctaattctgcatttgatgt-gttatagta--ttagtttttaatattaggaagagaaa--------------------------------------

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv10s0042g00140.t01 (Vitis vinifera), 5'ss of exon 2
GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttacttaataagtgccctgaaacttagtctttttgttctctttgttagttgacattgctaaggctaccttgtagttactttgaggaagtcactttgttttttacctcttacctattttgtgtgttggacag
|| ||| |||| ||||||||| | ||||| ||   |||||| |||||||||||||| ||||| |  ||||||||||| |||||||| |||||   ||  |  | |  ||           |  | | |||||    |    ||  || | | |  ||| |   | |||        ||  |||||||| | |||||    |                  
GGGAGGTTATTCACAGGAGCTGCTATTGGCCTACTCATAGCAGGAGGAGCTTATGTGAGTACCGTGGATGAAGCAACTTTCTGgta-tttac---attggatctccaaa-----------tgatacactttg---atcagaatcactgaagat-tcttttgtctgcttctcattgatc-ttttgttttattcctctactatga----------------

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|86073993|gb|DR369750.1|DR369750
EST:     GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG                         TGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
genomic: GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttact ... tgttggacagTGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
EST: gi|19875233|gb|AU236064.1|AU236064
EST:     CCNTAGCCTGGAGGAGCTTATGTTANTACTGCAGATGAAGCAACCTTCTG                         TGGGTGGCTATTCAACGCAACAAAGGTTGGTGAATCCTTTCTTTGCTCTT
genomic: CCATAGC-TGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttact ... tgttggacagTGGGTGGCTATTCAACGCAACAAAGGTTG-TGAATCCTTTCTTTGCTCTT
EST: gi|86073991|gb|DR369748.1|DR369748
EST:     CCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCCTTCTG                         TGGGTGGCTATTGAACGCACCAAAGG
genomic: CCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACC-TTCTGgtactttact ... tgttggacagTGGGTGGCTATTCAACGCAACAAAGG
EST: gi|86073994|gb|DR369751.1|DR369751
EST:     GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG                         TGGGTGGCTATTCAACGCAACAAAGGNTGTGAATCCTTTCTTTGCTCTTCT
genomic: GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttact ... tgttggacagTGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
EST: gi|86070492|gb|DR366249.1|DR366249
EST:     CCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTTCTG                         TGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTC
genomic: CCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTT-CTGgtactttact ... tgttggacagTGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTC
EST: gi|116483519|gb|EG526111.1|EG526111
EST:     GCCATAGCTGGAGGAGCTTATGCTAGTACTGCAGATGAAGCAACCTTCTG                         TGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
genomic: GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttact ... tgttggacagTGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
EST: gi|86073990|gb|DR369747.1|DR369747
EST:     GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG                         TGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
genomic: GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttact ... tgttggacagTGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
EST: gi|86073995|gb|DR369752.1|DR369752
EST:     GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG                         TGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
genomic: GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttact ... tgttggacagTGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
EST: gi|86073992|gb|DR369749.1|DR369749
EST:     GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG                         TGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT
genomic: GCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttact ... tgttggacagTGGGTGGCTATTCAACGCAACAAAGGTTGTGAATCCTTTCTTTGCTCTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTGgtactttacttaataagtgccctgaaacttagtctttttgttctctttgttagttgacattgctaaggctaccttgtagttactttgaggaagtcactttgttttttacctcttacctattttgtgtgttggacag

- - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA