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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttctatatccatttaaagtgtttcaataattactaagctcgaaacaaatatttcttgtag

Basic information

species Arabidopsis thaliana
transcript AT5G26120.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os11g03734.1 (Oryza sativa), 5'ss of exon 6
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagg---gatttttttcttttcggttctatatccatttaaa-gtgtttcaataattactaagctcgaaacaaatatttctt-gtag------------
||| |||||  |  |  | ||||||||||||||||| || ||||| ||||||||| | |||||||| ||||||||||||||  | | ||| ||  | || ||| ||   ||||  | ||   |  ||||| | |   | | |   | | | |  | ||  | |  |||||      || ||||  ||             
GAAGGAAACTATTGGTCCATGGGAAGAGAGACCTGGGCACTATGGAGATGTTTGGCACTACTGGACCGATGATGGCCTTGGGTATTATGACTTTCTCCAGgtatggattgattaatgtcaaatgagttctctcttggtctcatcatatctgatcatttgtttacttcgaactgttcatgtcttcataaatcttgctgaag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttt----tcttttcggttctatatccatttaaagtgtttcaataat-tactaagctcgaaacaaatatttcttgtag-------------------------
||  ||| |  |  |  | ||||||||||| ||||| || | ||| ||||||||| | |||||||||||||||||||||||  | | ||||||  | || |||   | ||  ||    |  || | |   |  ||    |||    ||   ||| || || |    | ||     |||||| |   |                          
GAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAATTTCTCCAGgtactagtttacttgacattattcctgcctttcattttcttatcacgtcctaatcatatattgcctttgagttctatatttttctaatgaaaactttgaactccacatcaaag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttt----tcttttcggttctatatccatttaaagtgtttcaataat-tactaagctcgaaa-caaatatttcttgtag--------------------------
||  ||| |  |  |  | ||||||||||| ||||| || | ||| ||||||||| | |||||||||||||||||||||||  | | ||| ||  | || |||   | ||  ||    |  |||| |  ||  ||    |||         ||| || || |    | |||  | | | ||| || ||                           
GAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATATTATGAGTTTCTCCAGgtaccagtttagttgacattatttccgcccttcattttcttatcactccctaatcatatattgcctttgaattctatttttttttctaatgaaaaatttgaactctacatcaaag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os12g03480.1 (Oryza sativa), 5'ss of exon 6
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaaggg---atttttttcttttcggttctatatcca---tttaaagtgtttcaataattactaagctcgaaacaaatatttcttgtag
||| |||||  |  |  | ||||||||||||||||| || ||||| ||||| ||| | |||||||| ||||||||||||||  | | ||| ||  |  | ||| |||   |||  | |    | |||| | | |       |     | | |||  | ||  | |  || |||    | ||  |   ||
GAAGGAAACTATTGGTCCATGGGAAGAGAGACCTGGACACTATGGAGATGTCTGGCACTACTGGACGGATGATGGCCTTGGGTATTATGAGTTACTCGAGgtatgggttgattaatgtgaaatgggttttttcttttggtctcggcatatctcaccatttgtttacttcaaaa----tgttcatgaaag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttc-----tatatccatttaa---agtgtttcaa-taattactaagctcgaaacaaatatttc----ttgtag
||  |||||| |  || ||||||||||||||||||| || | |  |||||||||||| || |||||||||||||| || |||   ||||| ||| ||||||||||  |  |  | |   | || ||     |  |  ||   ||   | ||  |||| |||  | ||||||   |     | ||||    ||||||
GAGTGAAACCATTGGACCTTGGGAAGAGAGACCTGGTCACTTTAATGATGTTTGGAATTATTGGACTGATGATGGACTAGGCTTTTTTGAGTTCCTTCAAgtaagtaaaatgctccagcttggctcagaactgaaagcagccaaataattgcatcaactaaccattaagctgatacacgttgtttcattattgtag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os11g03780.2 (Oryza sativa), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgt--aagggatttttttcttttcg---gttctatatccatttaaagtgtttcaataattactaa------gctcgaaacaaatatttcttgtag--
||  |||||  |  |  | |||||| |||||||||| || | ||| ||||||||||| || ||||| ||||||||||| ||  | |  || ||  | || ||  | |  | ||  | |  |  |   ||| | | | ||| |    || |   |  ||  ||||        |   | | ||  |||| || |   
GAGGGAAACTATTGGTCCCTGGGAACAGAGACCTGGGCACTTTGGAGATGTTTGGAATTATTGGACCGATGATGGCCTAGGATATTACGAGTTTCTCCAGgtgtatgttagttaatgccatctgagtgtttttttttcatctcttctgctatcaacatatctaacgaaatatttctaccgaaattttcatggaaag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G077299_T01 (Zea mays), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttctatatccatttaaagt--gtttcaataattactaagctcgaaacaaatatttcttgtag--
|| |||| |  |  |  | ||||||||||||||||| || |  || ||||||||| | |||||||||||||||||||||||  ||| ||||||  |||| ||    | || |  |  ||  | |      | | ||    ||  || ||   | | || |   |  |  |  | || |     |   
GAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGCCTTGGATACTATGAATTTCTTCAGgtgccagtttatactgcttctgttcgagctttccttccctgttggtgtcctcactgacaacaattaactctgaaatctacatcaaag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G006130_T03 (Zea mays), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatt--------tttttcttttcggttctatatccatttaaagtgtttcaataat-tactaagctcgaaacaaatatttcttgtag--------
|| |||  |  |  |  | ||||||||||| ||||| || |  || ||||||||| | ||||||||||||||||| |||||  | | ||| ||| |||| |||   | ||        |   | | ||   || | | |||  | |       | | || | || | |  || |    ||   ||   |  |        
GAGAGAGTCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagtttacactgcttcactttatttatttttctttcctatcatgacccctaagtattatattgaaatctacgtcaaagcttgcggaggacctgggt

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G006130_T02 (Zea mays), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttctatatccatttaaagtgtttcaataattactaagctcgaaacaaatatttcttgtag--
|| |||| |  |  |  | ||||||||||| ||||| || |  || ||||||||| | ||||||||||||||||| |||||  | | ||| ||| |||| |||   |  |||   ||  |    | ||| |   |||      | |||  |    |||||    | |   | || |     |   
GAGAGAATCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccag--tttacactgcttcactttatttatttttctttcctatcatgaccccctaagtattatattgaaatctacgtcaaag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G006130_T01 (Zea mays), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttctatatccatttaaagtgtttcaataattactaagctcgaaacaaatatttcttgtag--
|| |||  |  |  |  | ||||||||||| ||||| || |  || ||||||||| | ||||||||||||||||| |||||  | | ||| ||| |||| |||   | ||    |  ||    || | |||   | |    | |    || |   |||||    | |   | || |     |   
GAGAGAGTCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTGGCATTACTGGACTGATGATGGGCTTGGATATTATGAGTTCCTTCAGgtaccagtttacactgcttcactttatttatttttctttcctatc---atgacccctaagtattatattgaaatctacgtcaaag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA03G27460.3 (Glycine max), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttctttt-----------------cggt-tctatatccatttaaagtgtttcaataat-tactaagctcgaaaca-aatatttcttgtag--------------------
||||| | | ||  || | ||||| ||||||||||| || | |||||||||||||| |||||||||||||||||| |||||| | | ||| ||  | |||||||| |  | ||||| | |                  | | |  ||||| | || || |  |    |  | | ||| ||| |  | |  |||| | || |                      
GAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGCTATTATGAGTTTCTCCAAgtaagtgcctcttttcatatattgtagctgaggaatatgatgttcatatctagttgaattactcttgttttgtgctatgctagtgaaatgatatatattattattattattatttttgagcag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA19G30450.1 (Glycine max), 5'ss of exon 8
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttc------------------ttttcggttctatatccatttaaagtgtttcaataattactaagctcgaaaca-aatatttcttgtag--------------------
||||  | || |  || | ||||| ||||||||||| || | |||||||||||||| |||||||||||||||||| |||||  | | ||| ||  | |||||||| |  | ||| |                  || |    |   |||| | |  || |  |  | |  |  ||| ||| |  | |  |||| | |  |                      
GAAAACATCCATTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTGGATGTACTGGACTGATGATGGACTTGGTTATTATGAGTTTCTCCAAgtaagtgcctctttacatatattgtagcttaggattatgatgttcgtatctagtcgaattactctagttgt-gctatgctagtgaaatgatatatataattattattataatttttgagcag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA03G27490.1 (Glycine max), 5'ss of exon 7
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttctatatccatttaaagtgtttcaataattactaagctcgaaacaaatatttcttgtag--
|||||| |  ||  || | ||||||||||||||||| || | ||||||||||||||  || ||||| ||||| ||  ||||  | |||||     ||||||||||    ||| || |  |       | ||    ||    | ||   | | | | | |     |  ||  | ||   |||    
GAAAGATAGTGTTGGACCCTGGGAAGAGAGACCTGGTCACTTTGGTGATGTTTGGAGTTATTGGACAGATGAAGGATTTGGTTATTTTGAGGGTCTTCAAgtaagtccatttattatgataacaatcacattttgttgt--tattgtgaaattcaatcataataagccattttttgtgtgtgtag

upper sequence: AT5G26120.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 5'ss of exon 9
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttctatatccatttaaa-gtgtttcaataattactaagctcgaaacaaatatttctt--gtag------------------------
|||| | ||  |  |  | ||||| ||||||||||| || | ||||||||||||||||||||||||||||||||| |||||  | ||||| ||| |||||||| |  || ||   | | ||  || |  |    ||||    | | | | | |||    |  |   |  | ||  | |||  |||                         
GAAACAGACAATTGGGCCCTGGGAGGAGAGACCTGGACACTTTGGTGATGTTTGGAAGTACTGGACTGATGATGGACTTGGTTATTTTGAGTTCCTTCAAgtatgt-atcttccacctgtcaattgtgaaagattttatttatatcttagtgattgtacaatttccatgagatgctgcttaggtaatttacaaatgttttgtttctgtag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGAAACCGTGAGAGCTTGGGAAGAGAGACCTGGCCATTATGGTGATGTTTGGAAGTACTGGACTGATGATGGCCTTGGCCACTTTGAATTCTTTCAAgtaagggatttttttcttttcggttctatatccatttaaagtgtttcaataattactaagctcgaaacaaatatttcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG