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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagttatacatacaaaccttatatatctgactatgatgaataaaag

Basic information

species Arabidopsis thaliana
transcript AT1G07670.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os05g02940.1 (Oryza sativa), 5'ss of exon 2
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagt-tatacatacaaaccttatatatctgactatgatgaataaaag------
|||| |||||| ||||  | || ||||| ||||| || ||||||||||| || ||||||||||| ||||| || || ||||||||||| || |||||||||| |||  ||| |       | | | |   | |||  |    | |||| |     | | |      ||| ||| | || |    |  || | |        
AGGCCTCTGACATGGTTCTTGCTGATGACAATTTTAGTACCATTGTTGCGGCAGTTGGTGAAGGAAGGTCTATTTACAACAACATGAAAGCTTTCATCAGgttagtgatctcagagcctgtttttgttgttgttctcactttttgcttcaacacttgcttttgtcacttctat-tttggcagaaacaaacagactaatgct

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g17310.1 (Oryza sativa), 5'ss of exon 6
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagttatacatacaaaccttat--atatctgactatgatgaataaaag---------
| || || ||  ||||  | ||||||||||| ||||| || || || ||||||||||||||||| ||||| |||||  |||| |||||||| || || ||||   || |  ||||  |  ||||  |  | ||| || ||  | | | |  |   |||    ||    |    | || |   |||  |  || | |         
AAGCTTCAGATATGGTTCTTGCAGATGATAACTTCAGTACAATAGTCGCAGCTGTTGGTGAAGGGAGGTCAATCTACGACAATATGAAGGCATTTATAAGgtacatcat--tatgccagctatggctaaccctttct-tgctttgttagcatctgacaagtcaataaaaatgctgtcagttaatgtgggctatatgttattgcag

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G141704_T01 (Zea mays), 5'ss of exon 2
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggct-tgagttatacatacaaaccttatatatctgactatgatgaataaaag
| || || ||  ||||  | ||||||||||| ||||| || || || ||||| ||||||||||| ||||| || || |||||||||||||| || || ||||  || ||   ||     ||    |  | | ||  | ||  |   | |  |||| |   | | |   |   |      |||| |||||    ||
AAGCTTCAGATATGGTACTTGCAGATGATAACTTCAGTACTATAGTCGCAGCAGTTGGTGAAGGGAGGTCTATTTACAACAACATGAAGGCTTTTATTAGgtctgtttttggataagctatggccaaacttttt--tgtgcataattgttggttaaattaaaatatgctgagtcatgtgctat-atgaactgcag

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G056014_T01 (Zea mays), 5'ss of exon 6
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgt-------gagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagtta--------tacatacaaaccttatatatctgactatgatgaataaaag--
|||| |||||| |||||||||| || || ||||| |||||||| ||| | || || |||||||| || || ||||| ||||||||||| || ||||| ||||       |||  | |||   |||  | |  |  | |  |  ||   ||   ||  |           |     ||  | | |  |  ||| ||     |  |       
AGGCGTCTGACATGGTGTTGGCTGACGACAATTTTAGCACCATAGTTTCTGCAGTCGGTGAAGGAAGATCGATCTACAACAACATGAAAGCTTTCATAAGgtctgtgctgagcttgctttgattat-tgttcacactttgtagtactcgtacttttcgcccccttcccttgtgggcattcttgacgtccctgtcttcctcggctgccgcag

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA19G35960.1 (Glycine max), 5'ss of exon 6
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttat-gttacata---tgtatgcctcttcctatgggtggcttgagtta-tacatacaaaccttatatatctgactatga-tgaataaaag
| || || ||  |||||||||||||||||||||| ||  | |||||||| ||||||||||| || || || ||||| || || ||||||||||| ||||||||| |||| || | |||| |||   | |   |   | |  ||  ||  ||   |  | || |    ||  |  ||||||    | |   | |||    |
AAGCTTCAGATATGGTGTTGGCAGATGATAATTTTAGTTCAATTGTTGCTGCTGTTGGTGAGGGTAGATCTATCTACAATAATATGAAGGCCTTTATCAGgtgattcttattgtcgttaaataacttatccacaattccacataagtcactattgcaaataaaggataatttgctatatcactttctctctcaatctttg

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA03G33240.1 (Glycine max), 5'ss of exon 6
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttat-gttacata---tgtatgcctcttcctatgggtggcttgagttatacatacaaaccttatatatctgactatgatgaataaaag---
| || || ||  |||||||||||||||||||||| ||  | |||||||| ||||||||||| || || || ||||| || || |||||||| || ||||||||| |||| || | |||| |||   | |   |   | |  ||  |   ||   |  | | | |  |   |||  ||| | ||| |       ||      
AAGCTTCAGATATGGTGTTGGCAGATGATAATTTTAGTTCAATTGTTGCTGCTGTTGGTGAGGGTAGATCTATCTACAATAATATGAAGGCTTTTATCAGgtgattcttattgtcgttaaataacttatccacaattccacataagccactattgcaa-ataaaggataattagctatatcactttctctctcaatctttg

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv06s0004g03900.t01 (Vitis vinifera), 5'ss of exon 6
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagttatacatacaaaccttatatatct-gactatgatgaataaaag-------
| || |||||| |||| ||||||||||||||||| | ||| || ||||| ||||||||||||||||| ||||| || ||||| |||||||| || |||||||  |  ||||| |||  |||| | |            |||  |||||     ||  | | | |    |  || || || | ||| || |            
AAGCCTCTGACATGGTCTTGGCAGATGATAATTTTAACACAATAGTTGCTGCTGTTGGTGAAGGCAGATCCATTTACAACAATATGAAGGCTTTTATCAGgtttga-ttcttttgt-gcataagaaaattcagctacctggtaggcttacaaaattgacatataatacaattacctagaatgtgaagagtgttcactgagaa

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv08s0040g02830.t01 (Vitis vinifera), 5'ss of exon 6
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagttatacatacaaac-cttatatatctgactatgatgaa--taaaag------
| || |||||  ||||||||||||| |||||||| || || || ||||| |||||||| |||||  | || ||||| ||||| |||||||| || |||||||   | |  ||   || |   | | ||     |   |  | ||       |   | |||  |    || | | | ||||  || || |  |   ||      
AAGCCTCTGATATGGTGTTGGCAGACGATAATTTTAGTACAATAGTTGCTGCTGTTGGGGAAGGGCGATCTATCTACAACAATATGAAGGCTTTTATCAGgtttatttctttgcattcctggtctctgtggtctgtgacagatg---cagatctgagataagattatttgtttttgtgacagtggtggagttcttagtcacta

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EDP06981 (Chlamydomonas reinhardtii), 5'ss of exon 20
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacata-------tgtatgcctcttcctatgggtggcttgagttatacatacaaaccttatatatctgactatgatgaataaaag
||||    ||| ||||| |||| || || || |||||| |||| || || || || |  || ||| |  ||||||| ||||||||||||||||||||| ||||||       | |  | |         |||  |      |    ||  ||   | ||| |   | | |    | || |   ||       |       |
AGGCCAGCGACATGGTGCTGGCGGACGACAACTTCAGCTCCATCGTGGCGGCGGTGGCGGAGGGCCGCGCCATCTACAACAACATGAAGGCCTTCATCCGgtgagggaggggagggcagagggaagggctgtggggagagccaagcggaggggaggtgttgtttgttcgagaact-taaaagcgagggctgagggcggggg

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: PP1S78_99V6.2 (Physcomitrella patens), 5'ss of exon 8
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagttatacatacaaaccttatatatctgactatgatgaataaaag
||||| | ||| ||||| | |||||||||||||| ||||| ||||| ||||||||||| |||||  | || || || || || ||||||||||| |||||||| ||  | | || | | | |||  |     |       | |   | || ||| | ||   ||   ||   | |||| | ||   |   | ||
AGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGGCCTTTATCAGgtgggtaatttgatttaataaatgagttgtattaggctgagcttattagaattaaaaat-tgaattcta---acctgatt-tgtgaacctacag

upper sequence: AT1G07670.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: PP1S248_28V6.1 (Physcomitrella patens), 5'ss of exon 6
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagttatacatacaaaccttatatatctgactatgatgaataaaag
||||| | ||| ||||| | |||||||| ||||| ||||| ||||| ||||| ||||| |||||  | || || || |||||||||||||||||||| ||||| ||  | ||||  ||   |||      | ||     | ||   |||     |   ||| |      | |  ||||   ||  ||   | ||
AGGCAGCCGACATGGTGCTTGCAGATGACAATTTTAGCACTATTGTGGCAGCCGTTGGAGAAGGTCGTTCTATATACAACAACATGAAGGCCTTCATTAGgtgcgtgattttatactaaggatg---attttttgagtggagtattttggaaattgagtaccagaa--gtttgactgaagttgtggatctacag

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|164153279|gb|ES101088.1|ES101088
EST:     CTATAACAACATNAAGGCCTTCATCAG                         GTACATGATCTCTTCCAACATCGGTGAGGTTGCATCGATATTCTTGACAGC
genomic: CTATAACAACATGAAGGCCTTCATCAGgtgagtcttc ... tgaataaaagGTACATGATCTCTTCCAACATCGGTGAGGTTGCATCGATATTCTTGACAGC




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGGCCTTCATCAGgtgagtcttcttatgttacatatgtatgcctcttcctatgggtggcttgagttatacatacaaaccttatatatctgactatgatgaataaaag

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