Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaaatttttttctgaattcttctctttctttgagtatcgtcaatttgatattgtgtatgtttagatctgagagttgtttgactagatctttgattcatttatgctaattttggttttgatttgccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATATGGGATTTTCCTCTGCATCGATTGTTCAGCTACTCACCGGAATCTTGGTG

Basic information

species Arabidopsis thaliana
transcript AT4G17890.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17890.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 1
-----------------------------------------------gtaatcaaattt--ttttctgaattcttctctttctttgagtatcgtcaatttgatattgtgtatgtttagatctgagagttgtttgactagatctttgattcatttatgctaattttggttttgatttgccaattt-agGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATATGGGATTTTCCTCTGCATCGATTGTTCAGCTACTCACCGGAATCTTGGTG
                                               ||      ||||  |||  |  | |||   ||||   |  ||    ||   || |     | |   || ||||||| ||      ||      | |||||||  |  ||    ||     ||||  |||   ||||| || | || |||||||| | ||||||||| || || ||||| || || || |||||||| ||||||||||||||||| || ||   |||||| | ||| || |
gttttttgtttataattttgaatttcaatttgagtgcataatcgttggttccgtgatttcgtttaatatagtctgaacttttcgtttgtggtttctgatttacgagatctggtttcagatctgtgatacccgtggtagtgtgtttgatttttgaatttgtatggcttttttttttttttaatttcagATGTGTTTCGATTGCAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCG

upper sequence: AT4G17890.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 1
---------------------gtaatcaaatttttttctgaattcttctctttct---ttgagtatcgtcaatttgatattgtgtat--gtttagatctgagagttgtttgactagatctttgattcatttatgctaattttggttttgatttgccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATATGGGATTTTCCTCTGCATCGATTGTTCAGCTACTCACCGGAATCTTGGTG
                      |      ||||||   ||  ||||| | ||| |   |||  | | |    | || | ||| |     ||| |||||||   |||    || | |||||  | ||  |||||  |  || |  ||||| ||      ||||| | || || ||||||| ||||||||| || |||||||| || || || |||||||| |||||||||||||| || || ||    ||  ||| |||||| |
gtctgttctttactgaatttcttcgcggtatttttaaatgttttcttttgtttttattttggtttttggttttctgttcttgagatctggttcagatctggaggtttcgcgattggatctcggttt--tttattttgtttct--ttttggtt------tttagATGTGTTTTGATTGTAATGCGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGG
















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|116481523|gb|EG524115.1|EG524115
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015086|gb|DR310832.1|DR310832
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015069|gb|DR310815.1|DR310815
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015085|gb|DR310831.1|DR310831
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015088|gb|DR310834.1|DR310834
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015079|gb|DR310825.1|DR310825
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015073|gb|DR310819.1|DR310819
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015078|gb|DR310824.1|DR310824
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015066|gb|DR310812.1|DR310812
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015082|gb|DR310828.1|DR310828
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015063|gb|DR310809.1|DR310809
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015065|gb|DR310811.1|DR310811
EST:     CCGAC-AAANCATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015081|gb|DR310827.1|DR310827
EST:     CCGACNAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015089|gb|DR310835.1|DR310835
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015093|gb|DR310839.1|DR310839
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|125301200|gb|EL315285.1|EL315285
EST:     CCGAC-AAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGC
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGC
EST: gi|86015090|gb|DR310836.1|DR310836
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015077|gb|DR310823.1|DR310823
EST:     CCGACAAAADCATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015092|gb|DR310838.1|DR310838
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015076|gb|DR310822.1|DR310822
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015067|gb|DR310813.1|DR310813
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015064|gb|DR310810.1|DR310810
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015084|gb|DR310830.1|DR310830
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015094|gb|DR310840.1|DR310840
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015075|gb|DR310821.1|DR310821
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015071|gb|DR310817.1|DR310817
EST:     CCGACAAANNCATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015072|gb|DR310818.1|DR310818
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015074|gb|DR310820.1|DR310820
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015080|gb|DR310826.1|DR310826
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATSGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015070|gb|DR310816.1|DR310816
EST:     CGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCGTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATC-TGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015068|gb|DR310814.1|DR310814
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|19879081|gb|AU239912.1|AU239912
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|86015091|gb|DR310837.1|DR310837
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
EST: gi|152035562|gb|BP858031.2|BP858031
EST:     CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAG                         GTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT
genomic: CCGACAAAAACATTGTTTTCAGAAAACTCAAATCAAAATCTGAGAACAAGgtaatcaaat ... gccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactagatctttgattcatttatgctaattttggttttgatttgccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATATGGGATTTTCCTCTGCATCGATTGTTCAGCTACTCACCGGAATCTTGGTG
                   atttatgctaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaaatttttttctgaattcttctctttctttgagtatcgtcaatttgatattgtgtatgtttagatctgagagttgtttgactagatctttgattcatttatgctaattttggttttgatttgccaatttagGTCTGCTTCGATTGTAGTGCGAAGAATCCAACTTGGGCATCGGTTACATATGGGATTTTCCTCTGCATCGATTGTTCAGCTACTCACCGGAATCTTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT