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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAGGCTTTTCGATATGGAATTTACAGCAATGATGACATGGATGAGgtgatgttctcgtgtttccttttcatagctgctacgtgtgacttttctttggaaattagtattatccaagattttggccgcatatttcaataagttttgg...

Basic information

species Arabidopsis thaliana
transcript AT1G30470.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: LOC_Os01g40340.1 (Oryza sativa), 5'ss of exon 14
TGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAGGCTTTTCGATATGGAATTTACAGCAATGATGACATGGATGAGgtg-atgttctcg--tgtttccttttcatagctgctacgtgtgacttttctttggaaattagtattatccaagattttggccg-catatttcaataagttttgg
|||||| | ||  || || ||||||||||||||||| || || || || ||||||||||| || |||||||| || || ||||||||||| ||||| ||||||  |||| |      |||  |||   | |||   | |  |  | |   |    |  ||  | |      | ||||||   |   || ||  | | | |    
TGATGACTTCCGAGACAGGGATTATGATGTGGCAGCTCTTGCTAATAACTTGAGCCAGGCATTCCGATATGGGATATATAGCAATGATGATATGGAAGAGgtgtgtgttttgaatgattttgtttctcttgctttgatggtttgcgtcagtcaacatgtttctctgccagcacattttgttaggtttaatttgagaggat----

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: LOC_Os05g51490.1 (Oryza sativa), 5'ss of exon 16
TGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAGGCTTTTCGATATGGAATTTACAGCAATGATGACATGGATGAGgtgatgttctcgtgtttcc----------ttttcatagc-tgctacgtgtgacttttctttggaaattagtatt---atccaagattttggccgcatatttcaata-agttttgg-------------------------------------------------
|||||| | ||  || || || ||||||||||| || || || || ||  |||||||||| || || |||||||| ||||||||||||||||| || ||||||||  |||    || |            |||  |||| |||||    | || |  ||  ||||||  | | |    ||  |   | |     | |      ||| |||  |                                                   
TGATGACTTCCGAGACAGGGACTATGATGTGGCGGCACTTGCTAATAACCTGAGCCAGGCATTCCGGTATGGAATGTACAGCAATGATGACATTGAAGAGgtgattgtctgaacttgcagcagcctgagctttggtagcatgctagaatttacatacctgaggaaatgggcactgatgtcttatgctcttattaccttcactgatatagtcctctctagcattatggaacatgttagtaatgtgtcaatgtttgcttattgcag

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: LOC_Os01g40390.1 (Oryza sativa), 5'ss of exon 5
TGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAGGCTTTTCGATATGGAATTTACAGCAATGATGACATGGATGAGgtg-atgttctcgtg-tttccttttcatagctgctacgtgtgacttttctttggaaattagtattatccaagattttggccg-catatttcaataagttttgg
|||||||| ||  || || ||||||||||||||||| || || || || ||||||||||| || |||||||  || || | ||||||||| ||||| |||||| ||||     || |||  |||  || |||   | |  |  | |   |    |  ||  | |      | ||||||   |   || ||  | | | ||   
TGATGATTTCCGAGACAGGGATTATGATGTGGCAGCTCTTGCTAATAACTTGAGCCAGGCATTCCGATATGTGATATATAACAATGATGATATGGAAGAGgtgtatgtgtgaatgattttgtttctattgctttgatggtttgcatcagtcaacatgtttctctgccagcacattttgttaggtttaatttgagaggatt---

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: LOC_Os01g40370.1 (Oryza sativa), 5'ss of exon 3
TGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAGGCTTTTCGATATGGAATTTACAGCAATGATGACATGGATGAGgtg-atgttctcgtg-tttccttttcatagctgctacgtgtgacttttctttggaaattagtattatccaagattttggccg-catatttcaataagttttgg
||| || | ||  || |  ||||||||||||| ||| ||  | || || ||||||||||| || |||||||| || || ||||||||||| ||||| ||||||  |||     || |||  |||  || |||   | |  |  | |   |    |  ||  | |      | ||||||   |   || ||  | | | ||   
TGACGACTTCCGAGACATGGATTATGATGTGGTAGCTCTTACTAATAACTTGAGCCAGGCATTGCGATATGGGATATATAGCAATGATGATATGGAAGAGgtgtgtgtgtgaatgattttgtttctatcgctttgatggtttgcgtcggtcaacatgtttctctgccagcacattttgttaggtttaatttgagaggatt---

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GRMZM5G812498_T01 (Zea mays), 5'ss of exon 6
TGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAGGCTTTTCGATATGGAATTTACAGCAATGATGACATGGATGAGgtgatgttctcgtgtttccttttcatagctgctacgtgtgacttttctttggaaattagtattatccaagattttggccgcatatttcaataagttttgg-------
 || || | ||  || ||||| || ||||||||||| ||  | || ||| |||||||||| ||||||| ||| || ||||| ||||||||||| || ||||| || |||    ||    |||| | |     | | || |  ||     |     |     || |      ||||   || ||       | |  |  |        
CGACGACTTCCGAGACAGAGACTACGATGTGGCAGCACTCACTAATAATATGAGCCAGGCATTTCGATTTGGGATATACAGGAATGATGACATTGAAGAGgtaattttc----gtcagttttttacaagattttcttgagttttgaacatcatgttcttctttgtttt---tttttctcgaatgcgcaggtgaactgcgcatcatta

upper sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 5'ss of exon 16
TGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAGGCTTTTCGATATGGAATTTACAGCAATGATGACATGGATGAGgtgatgttctcgtgtttccttttcatagctgctacgtgtgacttttctttggaaattagtattatccaagattttggccgcatattt-caataagttttgg-
||||||||| || || |||||||||||||| ||||| |||||||| || ||||| ||||| || |||||||| ||||| || |||||||| |||||||||||  |||| |  | |      | |||   | ||   | |   |  |  ||  | ||   ||| ||  |    | |      |  ||| |   || |    | 
TGATGATTATCAAGACAGAGATTATGATGTTGCAGCTCTAGCAAATAACTTGAGTCAGGCATTCCGATATGGCATTTATAGTAATGATGATATGGATGAGgtattgtt-taatctaattagtccatctttactttctatttttggtactttaacatatatat-atatatatatatatatataagtttaccccaaatgcgagt

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|164065874|gb|ES116146.1|ES116146
EST:     TTTACAGCAATGATGACATGGATGAG                         GCCCAAGGCTCTATGGAACGCGATGATGAG
genomic: TTTACAGCAATGATGACATGGATGAGgtgatgttct ... tccactgcagGCCCAAGGCTCTATGGAACGCGATGATGAG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAGGCTTTTCGATATGGAATTTACAGCAATGATGACATGGATGAGgtgatgttctcgtgtttccttttcatagctgctacgtgtgacttttctttggaaattagtattatccaagattttggccgcatatttcaataagttttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA