Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcctttcatgtcttttgcatattactttctctagtgacaaatctacagttcaagatttggattatgattctatgtttatttgattaggtgcgt...

Basic information

species Arabidopsis thaliana
transcript AT4G14342.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 4
TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcctttcatgtcttttgcatattactttctctagtgacaaatctaca--gttcaagatttggattatgattctatgtttatttgattaggtgcgt----
 ||||| ||||| || || ||||| ||||| || |||||  |||| ||| | ||||||||||| || || |||||| |||| || |||||||| |||||||| ||     ||  | |  | ||  |   |   |||| ||  |  |  |  | |   |    || ||   |  |   |  || || || |      |  | |    
GGATAGCTATGCATCCTATATTGGGCACTATCCAATGCTGGCATATTTTTCCATTGCTGAGAATGAATCAATTGGAAGAGAGCGTTACAATTTTATGCAGgtatg-----ttaaaagcttattataacatgtcttctgta-cggtagttgaaaattatgttggacttatctggtttattaatattgatgtagaactgctcctaaaa

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G121942_T03 (Zea mays), 5'ss of exon 4
TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgt-ttgcctcctttcatgtcttttgcatattactt---tctctagtgacaaatctacagttcaagatttggatta---------tgatt----ctatgtttatt--tgattaggtgcgt-------------------------
 || |||||||| || || ||||| ||||| || |||||  |||| ||||| |||||||||||||| || || ||| ||||||| ||||||||||||||||| ||||||||  || | |  |  |  |||  ||    | | ||| || |      |   | || ||   | |||         | |||     |||||||| |   ||||      |                          
AGACAGTTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctccactcttcttctaagt-tatagctcaaatgtttagagaaattctagcgcataaatatcatggttaaaaaaaacctaattagacttatgtttactcacgattgaacctgaaatggacccctagtgtcttgtttag

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G121942_T01 (Zea mays), 5'ss of exon 4
TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgt-ttgcctcctttcatgtcttttgcatattactttctctagtgacaaatctacagttcaagatttggattatgattctatgtttatttgattaggtgcgt
 || |||||||| || || ||||| ||||| || |||||  |||| ||||| |||||||||||||| || || ||| ||||||| ||||||||||||||||| ||||||||  || | |  |  |  |||  ||        |    ||  |  ||  ||  | |   ||  | |    |    || ||       ||  |
AGACAGTTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAACGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtattgcctccactcttcttctaagt-tatagctcaaatgtttagagaaattctagcgcataaatatcatggttaaaaaaaacctaattagacttatgttt

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 4
TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcctttcatgtcttttgcatattactttctctagtgacaaatctacagttcaagatttggattatgattctatgtttatttgattaggtgcgt----
 || || ||||| || || ||||| ||||| || |||||  |||| ||||| ||||||||||| || || || ||| ||||||| |||||||||||||||||           | || || |    |  | |    | |||   ||||| || ||  |||  | ||||  || |||  ||  |  |    ||| ||        
AGACAGCTATGCCTCTTATATTGGGCACTATCCAATGCTAGCATATTTTGCCATTGCTGAGAATGAATCGATCGGAAGAGAACGTTACAATTTCATGCAGgtacataagacaacttgcctctactgttcttcaagttgtagct-caaatttatagaacaat-tctggagcataatt--attgtagtaaagttatgtcttaaaaa

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 3
-TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcctttcatgtcttttgcatattactttctctagtg-acaaatctaca-gttcaagatttggatt--atgattctatgtttatttgattaggtgcgt
 |||||| ||||| ||||| ||||| ||||||||| | ||   || ||||||||||||||| || || ||||||||| ||||||||||||  || |||||||||    |  ||||    | |||    || | |       ||| | | |  |  | ||      |||  |||     | |  ||| |  | |   |  |     
GTGATAGCTATGCATCATATATTGGGCACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcattttttttccctcccttttgtgataattgatagatgtgtatatactttgatgtgtgttgtttccatttggctagttcatgctcttctaccttcg-----

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G40200.1 (Glycine max), 5'ss of exon 3
TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcctttcatgtcttttgcatattactttctctagtgacaaatctacagttcaagatttggattatgattctatgtttatttgattaggtgcgt------
 ||||| ||||| ||||| ||||| ||||||||| | ||   || ||||||||||||||| || || ||||||||| ||||||||||||  || |||||||||    |  |||  | ||||   | | | |     |  | ||| | || | ||      ||| ||   | |     | ||  || || |||   | |        
AGATAGCTATGCATCATATATTGGACACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcatttttttttct-tcttcctcttgtga-----taaattgatagatgtgcatactttgatgtgtgctgtttccatctggctagttaattgtcttctacatttg

upper sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 3
TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcctttcatgtctt--ttgcatattactttctctagtgacaaatctacagttca-agatttggattatgattctatgtttatttgattaggtgcgt
|||||| ||||| |||||  |||| ||||||||  | ||  | || |||||||||||||| ||||| || |||||| |||| ||||||||||| ||||||||||||    | |  | |  |  ||| ||   | |||   |    |    | |  | |  | | |||  ||  | || | || |    | |||| |  |    
TGATAGCTATGCATCATATGTTGGCCACTACCCCTTACTGGCGTATTTTGCTATTGCTGAAAACGAATCAATTGGAAGAGAGCGCTACAATTTTATGCAGgtttgctctatgtattatagtagttgtattgcagttttctttaaaattgttgtttaatgaacaaattgagaaaaggaatttaag---gtatgatcatatttac

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|86025219|gb|DR320972.1|DR320972
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025225|gb|DR320978.1|DR320978
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|47828971|gb|CK118655.1|CK118655
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025228|gb|DR320981.1|DR320981
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGSCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025223|gb|DR320976.1|DR320976
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025236|gb|DR320989.1|DR320989
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025218|gb|DR320971.1|DR320971
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025217|gb|DR320970.1|DR320970
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025230|gb|DR320983.1|DR320983
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTGTCCTCCGGAAAGAGAAGAGGAATAGGT
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCT-TCCTCCGGAAAGAGAAGAGGAATAGGT
EST: gi|86025215|gb|DR320968.1|DR320968
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025220|gb|DR320973.1|DR320973
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGSGGSCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025231|gb|DR320984.1|DR320984
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|125020364|gb|EL092633.1|EL092633
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCT
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCT
EST: gi|86025222|gb|DR320975.1|DR320975
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025234|gb|DR320987.1|DR320987
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025229|gb|DR320982.1|DR320982
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025232|gb|DR320985.1|DR320985
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025233|gb|DR320986.1|DR320986
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025226|gb|DR320979.1|DR320979
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
EST: gi|86025221|gb|DR320974.1|DR320974
EST:     CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAG                         AAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG
genomic: CTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcc ... tgatttccagAAAATGCTATTACCCTGCGGCCTTCCTCCGGAAAGAGAAGAGGAATAGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcctttcatgtcttttgcatattactttctctagtgacaaatctacagttcaagatttggattatgattctatgtttatttgattaggtgcgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctct