Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag

Basic information

species Arabidopsis thaliana
transcript AT1G51690.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatcc-ttcgaatttacgaccatattcgttcatgcag
|| || |||||| ||||||| ||||||||||| |||||||||||||| ||||| || |||||||||||||| |||||||| || ||||| || ||| |||||||   ||   | | ||| |  | ||      ||| | |   ||  |  |      |  ||   | ||  |   | ||  |   |||||   | | |  ||| ||        
TCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCAAACATGGAGGACCTAACTGgtaaatttt---ccagtgtgagataagctaggcatgctgtgg-atttgccatttggcttccagttagttttaaatgttaaacacacgaat--gctatctaattggt--------

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag
|| || ||||||||||| || |||||||||||| ||||||||||||| |||||||| || ||| ||||||| || ||| | || ||||| || ||  ||||||   |||  || | | ||    |  |    |||| |  ||  |   |||   |  |||   ||  ||     |   ||      ||  | |   | |||            
TCAGCAGATGATTTGCGGATAAATCTTTGGAATTTGGAAATTAGCAACCAAAGTTTTAACATTATTGATGTTAAACCTACAAACATGGAGGACCTGACTGgtataactt--tcaaatcttcaaactcttagctatgctgactagtg-agtattaacatatacagccttttctcacacaatgggaaaaaaatgcagtcctatat----------

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagcctt---ggtctac--tgttatctcagtctaatatgttctcttatacggtac-ccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag
|| |||||||||||||| || |||||||||||| ||||||| ||||||||||||||||||||| ||||||| |||||| | || |||||||||||  ||||||   |||      ||||   ||  |  |  |||    || |    | |  | ||   |||  ||     |||  ||    |||  |   ||| || | |                  
TCAGCTGATGATTTGCGGATAAATCTTTGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACAAACATGGAAGATCTCACTGgtataacttccaaacctacaaagtatttcctatctgtgctgattatgtgtgtgataggtcatagatgtgaaaataagaaaatatactcaa-gaagttgcaa------------------

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G164185_T02 (Zea mays), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag
|| |||||||||||||| || ||||| |||||| ||||||| ||||||||||||||||||||| ||||||| |||||| | || |||||||||||  | ||||   |||      ||   | ||   ||| || ||| ||  | || |      ||   ||||     || | |  |     |    ||    || ||  ||  ||       
TCAGCTGATGATTTGCGGATAAATCTATGGAATTTGGAAATCAGCAATCAAAGTTTCAATATTATTGATGTTAAGCCTACAAACATGGAAGATCTCACCGgtataacttctaaacctacaaactt--tcttatctgtgctgat-tatgtgtgtgataggtcataggtgtgaaagaaaa----tatacataagggaacaagttgtttt------

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtcta-ctgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgat---atccttcgaatttacgaccatattcgttcatgcag
|| || |||||| ||||||| || ||||||||| | |||||||||||||| || || || ||||||||||| || ||||| || ||||| |||||| ||||||| | ||  ||   ||| || || | |    | ||  ||       | | ||  |||    |  |  |  |||  ||   |        ||| ||   ||  |            
TCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCAAACATGGAGGATCTAACTGgtaaacttttttcagtctgataactaattgcggtgtgcact-----gagcttcctgtttcctgtaaacattaatgttatcagactaggtagattcacagtcaagt------------

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttg-gtctactgttatc--tcagtcta-atatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag
|| ||||||||||||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| || ||||| |||||  | ||||||| |       |   |||||  | ||| || | ||  ||  |   | ||||    | ||  ||  ||||   |   |||      ||| | |   |                 
TCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACAGgtaagcttgataagaaaaattatcctttagtgtatacattatcagtatcagggtaaaactctaaaat-taattaatttatatagttcgagaaataattgca----------------

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag-
|| ||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| || ||||| |||||  ||||||||  ||     ||| || | |   | |  | ||    || | || || | |  ||       || | | |   || |   || | || | |  || |        | |   
TCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACTGgtaagtttt----cactattgtatttttatgctgtg----ctgaaactgttctctgttg----ataacttggtataattta--tccatttaaagggcaaaacttacagtaccat

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G20830.2 (Glycine max), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag-
|| ||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| || ||||| |||||  | ||||||  ||     ||| || | |   | |  | || |     | | | |  |  || ||     || | | |   || |   || | || | |  || |  | |  || ||| 
TCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACCGgtaagtttt----cactattgtatttttatgctgtgctga---aaatgttctctgttgat-----aacttggtataattta--tccatttaaagggcaaaaacatatatacagt

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA13G42800.2 (Glycine max), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag
|| || |||||| ||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||| |||||||| || ||||| |||||  | ||||||| ||| |  |     |  | |  ||    ||||  | |    |||| |  ||  | |  || |   ||    ||   |      ||      ||| | |         
TCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCAAATATGGAGGATCTGACAGgtaagc-ttgataaaaa---aaattatcctttattgttaacattattggtaac--ttggtaaaacactaaaattaattaatttatatggtttaagaaataattgca-------

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacg-accatattcgttcatgcag
|| ||||||||| ||||||| || ||||||||  ||||||||||||| ||||| ||||||||||||||||| |||||||| || ||||| |||||| |||||||   |    |||   ||||||   ||| ||||    |  ||  | ||    ||||    ||   ||   | | |    |||  ||| ||    | | |||           
TCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCAAATATGGAGGATCTAACTGgtaaaattattacta--attatct---tctgatattcagttatactctgtgtgtattttgtgtgtcttt---tccaaggcacttttaatatatttgctaaattgacct------

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagc-cttggtc----tactgttatctcagtctaatatgttctcttatacggtacccat---------ttatcatgcaatt---ggatgcgatatccttcga--atttacgaccatattcgttcatgcag--------
|||||||||||| || |||||||| | |||||  |||| || ||  | ||||||||||||||||||||| | |||||||  || |||||||| ||  | ||| |   | || ||    |   | | |||      | ||| ||   |||      | | |          ||||  |||||||   |||||  || |     ||  |||   |||  ||||  |  ||            
TCTGCTGATGATCTGAGAATTAATTTATGGAACATGGAGATCAGTGACCAAAGTTTCAATATTGTTGATATTAAGCCTGTCAATATGGAAGACCTTACAGgtgaatgcctgatcatgatgtagctctctttaatcagtatttttctttaattaacatcaaaatatacttgttattgtgcaattattggatgatattttgcatgatcattgttgactgtattgctggatttgtcacatcag

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacc---------catttatcatgcaattggatgcgatatccttcgaatt-tacgaccatattcgttcatgcag------------------------------------------------------------------------------
||||| ||||||||| |||| ||| | |||||||| ||| ||||  |||| |||||||||||||||||  |||| ||  | || |||||||| ||  | ||||  |  |    | |  ||| |||| || |  ||  || ||  |  |||| |         | ||||      |  ||     | | ||||| |  || ||         | |   |                                                                                   
TCTGCAGATGATTTGAGAATAAATTTATGGAATCTTGAAGTTAGTGATCAGAGTTTCAATATTGTTGACATCAAACCAACAAACATGGAAGACCTTACAGgtattctctcccatgcgtttagctca-tcaatgatcctccctcttttggtagctcatagtttcctttagagcttacctgatgaagctgtcctttgtcttatagagtggagattgaagacttgctacgttgtgaatcggagtggtcattgtaatccaatggactaacgcctttgggttactgggttggttttggttgaacag

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ09063 (Selaginella moellendorffii), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag
|||||||| |||||| |||| ||  | |||||| ||||||||||  | |  |||||||| ||||||||| ||||||| || || |||||||||||  | ||||        |||         ||||| |   ||||        | | |    |  | |  | ||                                               
TCTGCTGACGATTTGAGAATCAACTTATGGAATATGGAAATTAGTGACCTTAGTTTCAACATTGTTGATATCAAGCCAGCTAACATGGAAGATCTTACAGgtatagtcgcatct----ccgcttcagtttttcatgtctgacaggatgatgttaacct-ttgtacag----------------------------------------------

upper sequence: AT1G51690.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ08844 (Selaginella moellendorffii), 5'ss of exon 7
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag
|||||||| |||||| |||| ||  | |||||| ||||||||||  | |  |||||||| ||||||||| ||||||| || || |||||||||||  | ||||        ||| | |||    |||| |   ||||        | | |    |  | |  | ||                                               
TCTGCTGACGATTTGAGAATCAACTTATGGAATATGGAAATTAGTGACCTTAGTTTCAACATTGTTGATATCAAGCCAGCTAACATGGAAGATCTTACAGgtatagtcgcatctccggtt----cagtttttcatgtctgacaggatgatgttaacct-ttgtacag----------------------------------------------

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|86070772|gb|DR366529.1|DR366529
EST:     AAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTG                         AGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCT
genomic: AAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttg ... gttcatgcagAGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCT
EST: gi|86070771|gb|DR366528.1|DR366528
EST:     AGCCTGCGAAAATGGAAGATCTATCTG                         AGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCT
genomic: AGCCTGCGAAAATGGAAGATCTATCTGgtaagccttg ... gttcatgcagAGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCT
EST: gi|164226939|gb|ES196289.1|ES196289
EST:     AAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTG                         AGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAAT
genomic: AAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttg ... gttcatgcagAGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAAT
EST: gi|86070770|gb|DR366527.1|DR366527
EST:     AAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTG                         AGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCT
genomic: AAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttg ... gttcatgcagAGGTTATCACATCAGCAGAATTTCATCCTACCCATTGCAATATGTTAGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCGAAAATGGAAGATCTATCTGgtaagccttggtctactgttatctcagtctaatatgttctcttatacggtacccatttatcatgcaattggatgcgatatccttcgaatttacgaccatattcgttcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA