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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctactacgcaaatgatgagctgctgctattcatttccctacttctaggcatgctgttttcataccctgctgtaatatctaaaacgctttcctttcctatatcag

Basic information

species Arabidopsis thaliana
transcript AT2G20420.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 5
GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctact--acgcaaatgatgagctgctgctattcatttccctacttctaggcatgctgttttcataccctgctgtaatatctaaaacgctttcctttcctatatcag
|| ||||| ||||||||| ||||||| || ||||||||||||||  |||| |  || ||| | ||  ||||||| ||||||||    |  || |||   ||    || |  |  ||||||  ||  || ||   |    |||||  |    |  |  ||||  | ||      |   |           
GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCGgtatgtctttgaacacaagcaattttttg-tattgctcatttttctctttttatttactgagttttgttctattatttgaataaattaaggaagcttggta----------

upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 5
GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatg----ctactacgcaaa-----tgatgagctgc-tgctattcatttccctacttctaggcatgctgtt-ttcataccctgctgtaatatctaaaacgctttcctttcctatatcag------------------------------------------------------------
|||||||||||||| ||  ||||||| || ||||||||||||||| | || |  ||||| ||||    |||||| || ||| |    || || |  |||        |||  ||| |  ||| ||  |    | |  ||    | || |  |   |  |   || |    |  |  ||  |||| ||   | || |                                                              
GTTTACTTGTGTGAAAAGCTGTCACTTGTAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCAgtaagtttcctgcttcaaaaaattttctttgatttgcgttatatacaaatttaaattcttataacttctataatgtgtggctccctctttccttcattacagtttctttaaatttaaccaataaattttttttatgttgcttattataattcttttcttattatgtttttgcttttgcag

upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA13G18730.1 (Glycine max), 5'ss of exon 5
GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatg----ctactacgcaaatgatgagctgctgctattcatttccctacttctaggcatgctgttttcataccctgctgtaatatctaaaacgctttcctttcctatatcag---------------------------------------------------------------------------
|||||||||||||| ||  ||||||| || ||||||||||||||| | || |  ||||| ||||    |||||| || ||| |    ||| | |  || |  |    || |    || || | |  | ||  |  | | |   ||  ||| | || | |||| | |    | || |    | |  || |||                                                                           
GTTTACTTGTGTGAAAAGCTGTCACTAGTAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCAgtaagtttcctatttcaaaactttttctttgatttgctttatatacaaatttaaattcttacaacttctatatcatgtt-taatgtatggctccctctttccttcatta-cagtttctttaaatttaaccaataaaaaactatgttgcttattataattcttttctttttatgtttttgcttttccag

upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 5
GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctactacgcaaatgatgagctgctgctattcatttccctacttctaggcatgctgttttcataccctgctgtaatatctaaaacgctttcctttcctatatcag
|||||||||||||| ||  ||||||| |||||||||||||||||| | || | |||||| |||  |||||| || || ||| | | | |  |      | || |   | | ||  | ||  | ||| |  | ||| | | ||      | | |   |  | ||||     || |   |   |     
GTTTACTTGTGTGAAAAGATGTCACTTGTCAATGAGATGTACTTTGCTATCACTCTGGATCGTTCATCTGCGGGTCCAgtacgttcccaaac------tcagttttggatctttgtgtc--tgcttttgtgaatgatttgttttatttcagataggaagtttaaattatatttcccactctttctg-

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|116411794|gb|EG454386.1|EG454386
EST:     TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG                         TTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
genomic: TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctact ... cctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
EST: gi|116476127|gb|EG518719.1|EG518719
EST:     TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG                         TTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
genomic: TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctact ... cctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
EST: gi|86045986|gb|DR341741.1|DR341741
EST:     TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG                         TTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATNTTGCTGAG
genomic: TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctact ... cctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
EST: gi|86045998|gb|DR341753.1|DR341753
EST:     TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG                         TTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
genomic: TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctact ... cctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
EST: gi|125005302|gb|EL077571.1|EL077571
EST:     TCAATGAGATGTACTTTTCCATTA-TCTGGACCGTAAATCTGCTGGACCG                         TTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTG
genomic: TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctact ... cctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTG
EST: gi|124779998|gb|EH869941.1|EH869941
EST:     ATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG                         TTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
genomic: ATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctact ... cctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
EST: gi|86045989|gb|DR341744.1|DR341744
EST:     TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG                         TTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
genomic: TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctact ... cctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
EST: gi|116485864|gb|EG528456.1|EG528456
EST:     TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCG                         TTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG
genomic: TCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctact ... cctatatcagTTGATCATTGCCTGTAAAAAGGGTGGTACCAGTATTGAAGATCTTGCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGgtatgctactacgcaaatgatgagctgctgctattcatttccctacttctaggcatgctgttttcataccctgctgtaatatctaaaacgctttcctttcctatatcag

- - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA