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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaggctccccccctctcccttgattatgagatcacacagatgatacatgtttataaaccttcatctatcatatgtggaaacaacaagtgcagcatcaaagaacatgtagaacttaaacttttgatgttctccccagaattttaacctctatatatggttttctcgtcgatttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACAATACTCAAACTTATTTCTGGCGATCTGCAACCAAGCTCTGGAACAGTTTTCCGTTCTGCTAAG

Basic information

species Arabidopsis thaliana
transcript AT1G64550.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 12
gtaagaaggctccccccctctcccttgattatgagatcacacagatgatacatgtttataaaccttcatctatcatatgtggaaacaacaagtgcagcatcaaagaacatgtagaacttaaacttttgatgttctccccagaattttaacctctatatatggttttctcgtcgatttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACAATACTCAAACTTATTTCTGGCGATCTGCAACCAAGCTCTGGAACAGTTTTCCGTTCTGCTAAG
                                                                 | || | |  | |||     ||   | || ||  | |  |  ||| |  |  |     |||||| |||     |||   ||  |  | || ||      |  | |||   || ||||||| || || ||||| ||||| || || || ||||| ||||| |||||||| |||||||| ||||  ||||||||||| || || ||| | |||
--------------------------------------------------------------gtatgatttcttctttgttc---cactcattgtagtcttactg--catattaatgtctggtttttgaagttg----cagttcttccatttttaaatcc---ctcattgtcttgtttcagTGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 11
gtaagaaggctccccccctctcccttgattatgagatcacacagatgatacatgtttataaaccttcatctatcatatgtggaaacaacaagtgcagcatcaaagaacatgtagaacttaaacttttgatgttctccccagaattttaacctctatatatggttttctcgtcga--tttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACAATACTCAAACTTATTTCTGGCGATCTGCAACCAAGCTCTGGAACAGTTTTCCGTTCTGCTAAG
                                                                                    | |  ||        |    ||  |||| |   ||||| |  |||  |    |    |  ||     | | |  | |||| | || || |  ||||||||||| ||||||||||||||||| || ||||| ||||| ||  | ||| |||| ||||| || || || ||||| || || |||||||||||||||
--------------------------------------------------------------------------------tactatataaacctttttgtgggggagaatgttg---ttaaaataatgacatgactctgccatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCCAATGGTATTGGCAAGTCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGTTCTGCTAAG

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 11
gtaagaaggctccccccctctcccttgattatgagatcacacagatgatacatgtttataaaccttcatctatcatatgtggaaacaacaagtgcagcatcaaagaacatgtagaacttaaacttttgatgttctccccagaattttaacctctatatatggttttctcgtcga--tttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACAATACTCAAACTTATTTCTGGCGATCTGCAACCAAGCTCTGGAACAGTTTTCCGTTCTGCTAAG
                                                                                 | |  ||  |   | |  |    ||  ||||     ||||| |  |||  |    |    |  ||     | | |  | |||| | || || |  ||||||||||| ||||| ||||||||||| |||||||| ||||| ||  | ||| |||| ||||| || || || ||||| || || ||||| |||||||||
--------------------------------------------------------------------------------agtactaaataaacctgtgtgggggagaatgtta---ttaaaataatgacatgactctggtatattgtttatgtgttgaaggttatttcctcaatgtttgcagTGGTTGGACCAAATGGTATTGGCAAATCAACTATACTTAAGTTAATTGCTGGGGATCTTCAGCCCAGTTCTGGGACTGTCTTCCGATCTGCTAAG

upper sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 12
gtaagaaggctccccccctctcccttgattatgagatcacacagatgatacatgtttataaaccttcatctatcatatgtggaaacaacaagtgcagcatcaaagaacatgtagaacttaaacttttgatgttctccccagaattttaacctctatatatggttttctcg-tcgatttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACAATACTCAAACTTATTTCTGGCGATCTGCAACCAAGCTCTGGAACAGTTTTCCGTTCTGCTAAG
                                                                             | |   | ||     |   |||| | |   ||| |   | ||    ||||  |||| | |||  |  ||     || | || ||| | ||    | | ||||||||||| || || ||||| |||||||||||||| ||||||||| | ||| | || || || ||||||||||||||||| || |||||||| || |||
----------------------------------------------------------------------------gtcttttagcattttattaggcatgatactgcattt---atttgg--ttttattgtttttccct-atcttatttttccaaatctggatctccaaattgttttgcagTGGTTGGGCCAAATGGCATTGGTAAATCAACTATACTCAAATTGATTGCAGGGGAACTTCAACCAAGCTCTGGAACGGTATTCCGTTCGGCCAAG

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|164114234|gb|ES048848.1|ES048848
EST:     GTTGTTTAGGAACCTAAATTTCGGAATAGATCTGGACAGCCGTATTGCAA                         TGGTGGGACCCAATGGTATTGGTAAATCAACA
genomic: GTTGTTTAGGAACCTAAATTTCGGAATAGATCTGGACAGCCGTATTGCAAgtaagaaggc ... cgatttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgttctccccagaattttaacctctatatatggttttctcgtcgatttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACAATACTCAAACTTATTTCTGGCGATCTGCAACCAAGCTCTGGAACAGTTTTCCGTTCTGCTAAG
                 ttttaac  putative branch site (score: 2)
                                    ttttctcgtc  putative PPT
             agaattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaggctccccccctctcccttgattatgagatcacacagatgatacatgtttataaaccttcatctatcatatgtggaaacaacaagtgcagcatcaaagaacatgtagaacttaaacttttgatgttctccccagaattttaacctctatatatggttttctcgtcgatttgcagTGGTGGGACCCAATGGTATTGGTAAATCAACAATACTCAAACTTATTTCTGGCGATCTGCAACCAAGCTCTGGAACAGTTTTCCGTTCTGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT