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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttccacttcttgtctgtatcttagtactcatgcttagctctgttgtacttgattttgcggaagaaactacaatcgtcaatcttgcaaaaggatct...

Basic information

species Arabidopsis thaliana
transcript AT4G13430.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G010044_T01 (Zea mays), 5'ss of exon 11
AGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaag--ttccacttcttgtctgtatcttagtac---tcatgctt-agctctgttgtacttgattttgcggaagaaactacaatcgtcaatcttgcaaaaggatct
|||||||||||| ||||| || ||| |||| || || |||||||| |||||||| ||||| ||||||||  | ||||| || ||  | |||   ||  | |||||  | |    ||  |||    | |  ||||   ||||  || ||  ||  | | |      |    |    |  |  ||   |   ||||     ||     
AGAATGCAAAGATGTGAAGATCGACCGAGTCTATATTGGTTCTTGCACTGGTGGTAAGACCGAGGATTTCCTTGCTGCTGCAAAGGTGTTCTTAGCCTCGgtaagaatcctgaatcaggtcatggtgtatgtacctgtcatctttcagacctcctatcccatggctacttggcttacttgaaactttttttcttaatccag-----

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA20G34160.1 (Glycine max), 5'ss of exon 14
AGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttccacttcttgtctgtatcttagtactcatgcttagctct---gttgtacttgattttgcggaagaaact--acaatcgtcaatcttgcaaaaggatct
|||||||||  | ||||||||||||||||||||||| || || || |||||||||||||| || ||||||||||||||||| ||| |||||   || |  ||| ||      |  | ||| | || |     |  |  ||| |        || | || |||||  ||  || | |  | || | | |||  |      ||||  
AGAATGCAACAATGTGAAAATTGACAGAGTATACATTGGATCCTGCACTGGTGGGAAGACTGAAGATTTTATGGCTGCAGCAAAAGTTTTCTTAGCGGGGgtatgtctattataatttctttctcctgcactttctttttaacatgcaaactgcattt-attttatggtggatattggaaaaccattaatactct----ggattc

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 12
AGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttccacttcttgtctgtatcttagtactcatgcttagct--ctgttgtacttgattttgcggaagaaactacaatcgtcaatcttgcaaaaggatct
||| ||||| || ||||||||||||||||||||||| || |||||||| ||||| || ||||||||||| ||||||||||| ||| |||| |  ||| |||||||   ||  | ||  |   || ||     | |   ||  |    | || |     | ||| |      |     |  | ||  |  |  |      |  
AGAGTGCAAGGATGTGAAAATTGACAGAGTATACATAGGATCTTGTACAGGTGGCAAAACAGAGGATTTCATGGCTGCAGCAAAAGTTTTTCTGGCATCAgtaagcatcatattttcccatcatatttaacttaagttttcacaagatattattaacaacttttctagctgagtcctagacttctttactatatttatgt--

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 12
-AGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttccacttcttgtctgtat-cttagtactcatgcttag-ctctgttgtacttgattttgcggaagaaactacaatcgtcaatcttgcaaaaggatct-
  || ||||| || || |||||||||||||||||||| || |||||||| ||||| || || |||||||| |||||||| || ||| |||| |  ||| |||||||   ||  | |||  | | | | || | |  ||   | | ||  ||| ||   ||| ||       ||  |   ||     || ||   ||  | | | 
GGGAGTGCAAGGATGTAAAAATTGACAGAGTATACATAGGATCTTGTACAGGTGGCAAAACGGAGGATTTCATGGCTGCTGCAAAAGTTTTTCTGGCATCagtaagcatcatattttgaatattttcctattgcatatatatggtctaagttataaaagatgtta--acttaagttttgataa--gatattattaacagcttta

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 12
AGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttccacttcttgtctgtatcttagtactcatgcttagctctgttgtacttgattttgcggaagaaactacaatcgtcaatcttgcaaaaggatct
||||||||||||||||||||||||||| || || || || |||||||||||||| || || ||||||||| | |||||||| ||| |||| || ||  |||||||||   ||   |  ||     |        |    | | |   | || ||| ||||      |     |    | ||      |  ||    |  |
AGAATGCAAAGACGTGAAAATTGACAGGGTGTATATTGGATCTTGTACTGGTGGAAAAACTGAGGATTTTCTAGCTGCAGCCAAAGTTTTTCATGCTTCAgtaagtttttctagcttacttagcttcttcgaggacaacttgttacttcgttcttaatttgcattcattgtttcttgttgtggtatatctaatttcacat

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 12
AGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttccact-tcttgtctgtatctt--agtactcatgcttagctctgttgtacttgattttgcggaagaaactacaatcgtcaatcttgcaaaaggatct
|||||||||||| |||||||||||||| ||||| || || ||||| |||||||| || || ||||||||| | |||||||| ||| |||| || ||  | |||||||   || |||| |||   ||||  || ||   || ||    || ||||  || ||||       |   ||    | ||   |||      |  ||| 
AGAATGCAAAGATGTGAAAATTGACAGGGTATATATTGGATCTTGCACTGGTGGAAAAACTGAGGATTTTCTAGCTGCAGCCAAAGTTTTTCATGCTTCCgtaagtttttctatcttctcttgctcttctaggaccattgattgtaact-ttgttgttaatttgcatatcgtgtctgttgttgtgtgtctaatttcac-atc-

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|164160390|gb|ES180127.1|ES180127
EST:     GTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTT-CCACGCAGCA                         GGAAGAAAGGTCAAAGTTCCAACTTTCCTTGTCCCGGC
genomic: GTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttcca ... gttttatcagGGAAGAAAGGTCAAAGTTCCAACTTTCCTTGTCCCGGC
EST: gi|164212915|gb|ES156598.1|ES156598
EST:     GTGGGAANACAGAGGATTTTANGGCTGCAGCTAAACTTTTCCACGCAGCA                         GGAAGAAAGGTCAAAGTTCCAACTTTCCTTGTCCCGGC
genomic: GTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttcca ... gttttatcagGGAAGAAAGGTCAAAGTTCCAACTTTCCTTGTCCCGGC
EST: gi|163983492|gb|ES040206.1|ES040206
EST:     AAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCA                         GGAAGAAAGGTCAAAGTTCCAACTTTCCTTGTCCCGGCTACTCAGAAG
genomic: AAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttcca ... gttttatcagGGAAGAAAGGTCAAAGTTCCAACTTTCCTTGTCCCGGCTACTCAGAAG
EST: gi|124753464|gb|EH843594.1|EH843594
EST:     GTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCA                         GGAAGAAAGGTCAAAGTTCCAA
genomic: GTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttcca ... gttttatcagGGAAGAAAGGTCAAAGTTCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATGCAAAGACGTGAAAATTGACAGAGTATACATCGGTTCTTGTACTGGTGGGAAGACAGAGGATTTTATGGCTGCAGCTAAACTTTTCCACGCAGCAgtaagttccacttcttgtctgtatcttagtactcatgcttagctctgttgtacttgattttgcggaagaaactacaatcgtcaatcttgcaaaaggatct

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaagga