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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA

Basic information

species Arabidopsis thaliana
transcript AT1G45050.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 5
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtc-tgaaactaagaatatcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA
            |  | | | ||| || |      ||   |     | ||||  |    ||| || || | || |  |||| | | ||||| ||||      ||  |||||||||| ||||| || || ||||| ||||| | ||||||    ||||||||||| || |||||||| ||||||||||| ||||| ||||| || ||||   
-----------gttatagagcttcactgt------gtcctc-----tcctgtttaaatggagatcatgcatctgaccatatta-tatgtttattat---atgttggtgcagCAACGTCCTGCCGACAATGATCGCTATGTCAGGAACTGCCGCAATGGGAGGTCGCCGAAGGAGACCAGGTGGTGGTTTCATGATGACAAAGTGTGATTGG

upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 5
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgcctta----ttgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA
                          |||| | |  | ||  | |    |   | ||       ||||  | || || || ||   || | ||  |      |     |||||||||||||||   || || || || ||||| | ||| ||    ||||||||||| || |||||||| || |||||||||||||| ||||| || | |    
------------------------gttatt-atatataactaacacccttcccattttctttcgctga--ccaaaaacattaaaaggtatcttgctataatgtggtgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGATGACAAAGTGTAAGAGG

upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 5
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA
                            ||    | || | | |  ||   |   | |   |||  |   ||     | | | ||   |   ||      |  ||||||||||||||| || ||||||||||| ||||| | |||||||   ||||||||||| || |||||||| | ||||||||||||||||||||  || |||||  
---------------------------gttacatatttcctctacatatccttgttcaatcggt--gggtcttgctttctgactgcaatacatacatgtaccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGGTCACCAAAGGAGACCACGTGGTGGTTCCATGACGACACTGTGTGATGGG

upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 6
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgc--cttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA
                                   |||||  |   | || |  || |    || ||||     |  | |   | |    |  | | |    |  ||||||||||||||| || ||||| ||||| ||||| |||||||||   |||||||||||||| || ||||| ||||||||||||||||| ||||  || ||||   
-----------------------------------gttacatatttt-ctctacatcaccttgt-tgaattggtgggtcttgcttttgactgcaatacattaccgattgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG

upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgccttatt-gcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA
                 |||   |    |   ||   |||   |  || |   |  |  | | ||| |  | |     |         |   ||    |  || || |||||||||||| ||||| || || || ||||| | ||||||    || |||||||| || |||||||| || ||||||||||||||||||| ||| | |||  
-----------------gtgacacttagtcatcatactacttgatctattcaaacctcggtgctctcactccatagccagactctaactagctagaatgtattgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT

upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 5
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaata---tcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA
               | | ||||     |  || |  ||| | |  || |   |  |  | |  ||||  | |  |  |   || |  |   |   | | |   || ||||||||||| || | ||| || || || ||||| | ||||||    || |||||||| || |||||||| || ||||||||||||||||||| ||| | ||  |
--------------gtagcgtttagtctt--actaactactcgatctattaaaacctcagtgccctgactccataatcagactctaactagctaacaatgcat-ttgttgcagCAACGTCCAGTGGACAATGACCGCTATGTCAGGAACTGCCGCAACGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGACGACACGGTGTAATTGA

upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G018447_T02 (Zea mays), 3'ss of exon 5
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaata---tcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA----------
               | | ||||     |  || |  ||| | |  || |   |  |  | |  ||||  | |  |  |   || |  |   |   | | |   || ||||||||||| || | ||| || || || ||||| | ||||||    || |||||||| || |||||||| || ||||||||||||||||||| ||| | ||  |          
--------------gtagcgtttagtctt--actaactactcgatctattaaaacctcagtgccctgactccataatcagactctaactagctaacaatgcat-ttgttgcagcaacgtccagTGGACAATGACCGCTATGTCAGGAACTGCCGCAACGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGACGACACGGTGTAATTGAGCGCCTGTCA

upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 5
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA
     |  || || ||   | |||   |  |  || |||   |    |  |  |   || | |  ||  | |  |  |   |||   | |||  ||      | | ||||||||||||||  ||||| || || ||||| |||||||| |  ||||| || || || |||||||| ||||||||||||||||| ||||| || | ||   
-----tggttattatttaagattcttcag-gtgaatttaggtaggtcatcg--atccatcatgggtgtcatttcggct--taataactctttactttatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAT

upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
gttctttcttcttcttcgtgtttccctattgacaagtt-acccaaagtactg-tgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA
           || ||   | |||  || ||   | || |   |    | || |  || || |  |  |   |        | |||   |  ||| ||      | | ||||||||||||||  ||||| || || ||||| |||||||| |  ||||| || || || |||||||| ||||||||||||||||| ||||| || | ||  |
----------attatttaagattc--tactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgaggtctgaaactaagaatatcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA
                                ttttttattccgcctt  CT-rich tract
                    aatatcaatgtgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgccttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG