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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagtacttactaaagcagatacttcacactgtcattctcttgaaaatgttgaagctaatgtgcatgaaatcag

Basic information

species Arabidopsis thaliana
transcript AT3G59140.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os11g05700.1 (Oryza sativa), 5'ss of exon 1
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagtactt---actaaagcagatacttcacactgtcattctcttgaaaatgt---tgaagctaatgtgcatgaaatcag------
  |||| || |||||||| ||||||||| |||||||||| ||||| ||||||||||| || ||||||||||||||||| || || |||||||| ||| | ||||| |  |   | | |   |||    | | |  |        ||||  || |   | ||   ||  |  ||  | |         
TGTTCAGCTTGCTCGTGCACTATACCAAAATGCAGACATCTATCTTCTTGATGATCCTTTCAGTGCTGTTGATGCACATACAGCATCAAGTCTTTTCAATgtaaggatctcaaattcataaagaagtgtgaaatagagtgctatttgaccatttttttaaaaaaaagatatatatatttttttgtag

upper sequence: AT3G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os06g06440.1 (Oryza sativa), 5'ss of exon 2
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagtac------ttactaaagcagatacttcacactgtcattctcttgaaaatgttgaagctaatgtgcatgaaatcag
  |||| || |||||||| ||||||||| |||||||||| ||||| ||||||||||| || |||||||||||||| || || || |||||||||||  | ||||  |       ||  |||   |  |   |  || ||  |||        | ||||      ||  |   |    |   
TGTTCAGCTTGCTCGTGCACTATACCAAAATGCAGACATCTATCTTCTTGATGATCCTTTCAGTGCTGTTGATGCCCATACAGCATCAAGTCTGTTTAATgtaaagatcacaaattcataacaaatgtgtatttcagtgctatttgaccatgactgtttttcaaaacttttttttggtag-

upper sequence: AT3G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: AC234203.1_FGT004 (Zea mays), 5'ss of exon 2
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagtacttactaaagcagatacttcacactgtcattctcttgaaaatgttgaagctaatgtgcatgaaatcag
  |||| || ||||||||  |||||||| |||||||||||||||| || ||||| || || || ||||||||||| ||||| ||  | ||||| ||  | ||||||      |||     ||   |  || | |  |  || |   | | ||||| |   | |  ||   | |||
TGTTCAGCTTGCTCGTGCATTATACCAAAATGCAGACATTTATCTTCTCGATGACCCTTTCAGCGCTGTTGATGCCCACACAGCAACTAGTCTTTTTAACgtaagtggcagataacaatcatgaatttcaatat--tcatcataggatttttgaaacatctatttatttga-cag

upper sequence: AT3G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G111903_T02 (Zea mays), 5'ss of exon 4
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagtacttactaaagcagatacttcacactgtcattctcttgaa--aatgttgaagctaatgtgcatgaaatcag---
  |||| || ||||||||  | |||||  |||||||||| |||||||||||||| || || || ||||||||||| ||||| ||  | ||||||||  | ||||||  | |  ||| ||| |          ||  || || |  |  | |  |      ||  |  ||   ||  |   
TGTTCAGCTTGCTCGTGCATTGTACCAGAATGCAGACATCTATCTCCTTGATGACCCTTTCAGCGCTGTTGATGCCCACACAGCAACGAGTCTGTTTAATgtaagtg-tcaaaaaaacagctgtgaattgaagtatttatcatagactagtacttttaaaaaaatctattttattggcag

upper sequence: AT3G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G28910.1 (Glycine max), 5'ss of exon 3
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaa--gtacttactaaagcagatacttcacactgtcattctcttgaaaat-----gttgaagctaatgtg--catgaaatcag----
 |||||||| |||||||| || || ||  |||| ||  | |||||| | ||||||||||||||||||||||||||||| |||||  | | ||||||  | ||||    |  | |        | |  | ||| |    || | ||    ||      || ||  |||  ||    ||||||  |    
AATTCAACTTGCTCGTGCACTTTATCAGAATGCTGATGTATATCTCTTGGATGATCCATTTAGTGCTGTTGATGCACATACTGCCACTAATCTGTTTAATgtaatgacatcttcctttcttcacatattacatttatgttttatttgttattctttattcaaattaacatggttttgaaatttggcag

upper sequence: AT3G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G30490.1 (Glycine max), 5'ss of exon 4
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagta----cttactaaagcagatacttcacactgtcattctct-tgaaaatgttgaagctaatgtgcatgaaatcag--------
 |||||||| || ||||| ||||| ||  |||| || || |||||| | ||||||||||| ||||||||||||||||| |||||  ||| | ||||  | ||||  |     |   |    ||| |||| ||   | | | |   | | |  || ||    || ||          |||         
AATTCAACTTGCACGTGCACTATATCAGAATGCTGATATATATCTCTTGGATGATCCATTCAGTGCTGTTGATGCACATACTGCAACAAATTTGTTTAATgtaacaaaaacttcttttcttcaggtactacat-ttataacttggtgttagtatctttttacttatagatggcttttcaacggaacag

upper sequence: AT3G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G37160.1 (Glycine max), 5'ss of exon 2
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagta----cttactaaagcagatacttcacactgtcattctcttgaaaatgttgaagctaatgtgcatgaaatcag--------
 |||||||| || ||||| ||||| ||  |||| || || |||||| | ||||||||||| ||||||||||||||||| |||||  ||| | ||||  | ||||| |     |   |    ||| |||| ||  |     ||    | |  || ||    || ||          |||         
AATTCAACTTGCACGTGCACTATATCAGAATGCTGATATATATCTCTTGGATGATCCATTCAGTGCTGTTGATGCACATACTGCAACAAATTTGTTTAATgtaaggaaaagttcttttcttcaggtactacattcatatcttggtgttattatatttttacttatagatggcttttcaactggacag

upper sequence: AT3G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G28900.1 (Glycine max), 5'ss of exon 4
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagtacttactaaagcagatacttcacactgtcattctcttgaa--aatgttgaagctaatgtg--catgaaatcag----
 |||||||| || ||||| || || ||  |||| ||  | ||||| || ||||||||||| ||||||||||||||||| |||||  ||| | ||||  | ||||   | |  |      |  || |   |   |  | || |||    | | || |  | ||  ||    |||||   |    
AATTCAACTTGCACGTGCACTTTATCAGAATGCTGATGTATATCTGCTGGATGATCCATTCAGTGCTGTTGATGCACATACTGCAACAAATTTGTTTAATgtaatggcatcttcctttcgtcacatactataattgtgcttttgtgtcattctttactccaacatggttttgaaacttggcag

upper sequence: AT3G59140.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G37150.1 (Glycine max), 5'ss of exon 3
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagta-------cttactaaagcagatacttcacactgtcattctcttgaaaatgttgaagctaatgtgcatgaaatcag
 |||||||| ||||| || || || ||  |||| || || |||||| | ||||||||||  |||||||||||||||||||||||  ||| | ||||  | ||||  |        |   |    ||||||||  |     |  || | ||  |  | | || |    ||    |  |  |||
AATTCAACTTGCTCGCGCTCTTTATCAGAATGCTGATATATATCTCTTGGATGATCCATGCAGTGCTGTTGATGCACACACTGCCACAAATTTGTTTAATgtaatgagaaaaacttcttttcttcagatactatatttgcttttttttttttacttatagatggctttgaaacttca--cag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTCAACTCGCTCGTGCGCTATACCAAGATGCAGACATTTATCTCCTTGATGATCCATTTAGTGCTGTTGATGCACACACTGCTTCAAGTCTGTTCCAAgtaagtacttactaaagcagatacttcacactgtcattctcttgaaaatgttgaagctaatgtgcatgaaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT