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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG

Basic information

species Arabidopsis thaliana
transcript AT4G34660.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 2
--------------------------gttgtttttcttaagcttttgactagtttgaagttttgattacta--ttgattttggactcat-tcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
                           |||||||  || |   ||    | | || |    ||     |||   ||||  | |   ||  ||    |  ||||||||||||| ||||| ||||||||||||||||| ||||||||||| ||||| || || || ||||| |||||||
gttacctggttctttgatttcaattctttgttttcatttatagttgatgtcgatttatcccttctcccctaggctgatcatagctccaaatccaattgtgttttcagCATTATCAAAGGGATATTGTTCGTGGTGTAGAAGGTTATATTGTTACTGGATCCAAGCAAGTGGAAATAG

upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 2
--------------------------gttgtttttcttaagcttttgactagtttgaagttttgattact--attgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
                            | ||||| ||    ||||  ||    | | | | |   |  |    ||||  || | |   | |||      ||||||||||| ||||| |||||||| |||||||||||||||||||| || || || || || |||||||||||||
gttacttggtttttctgtacctaccctctatttttgtttgtgttttacctccacttatgctctccctgtttggctgataatgaaatatattgtt------tttcagCATTATCAAAGGGATATTGTCCGTGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG

upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 2
----------------------gttgtttttcttaagcttttgactagtttgaagttttgatta-ctattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
                       || ||||| || |  | | |   |  | ||  | |   ||  |   | |  |   | |   ||    |  | ||||||||||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| || ||||| |||||||
gtgacttggttctttgatttcaattcttttttttcatttatagttcatgtcgatttatcccttctcccctaagctgataatagctccaattgtggtttcagCATTATCAAAGGGATATTGTTCGAGGTGTAGAAGGTTATATTGTTACCGGGTCCAAGCAAGTGGAAATAG

upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 2
--------gttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggactcattcgttc--------------ttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
        ||| || |     | |  |  | |  | |     ||| ||  ||| | ||      |   || |                 ||  |||||||||||| ||||| |||||||| || ||||||||||||||||| || || || || || |||||||||||||
gttaattggtttttctgtaccaaccctctatttttgtttgtgttttatctctacttataccctccctgtttggctgataatgaaatatattgtttttcagCATTATCAAAGGGATATTGTCCGCGGTGTGGAAGGTTATATTGTAACTGGATCCAAGCAAGTTGAAATAG

upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 2
gttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggac--tcattcgttcttcgttttca---gCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
     ||     | || | | |||  | || |  | |  |   ||||  || |  ||  |  |   | |||   | |||   ||||| |||||| |||||||| ||||||||||||||||  |||||||| ||||| || |||||||||||||
----gttacacaatgcctcttacttctatgtaactgtcctgtatatttcttcttaacctttgtatatccttttctctcactagCATTTCCAAAGGGATATTGTCCGTGGTGTGGAAGGTTTCATAGTTACTGGGTCCAAGCAAGTTGAAATAG

upper sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 2
-----gttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
      |  |  | ||   | |  |   |   |  |  | || ||| |      || |  | |  |   |  ||   ||||||||||  ||||| ||||||||||||||||| ||||||| ||| ||||| ||||| ||||||||||||||||
gttgcttaatcctcctgtggttcatttgtgactcaatttgtttatttcctcaacttataaatttctatatcatt---tttcagCATTTTCAAAGGGATATTGTTCGTGGTGTAGAAGGTTTTATCGTTACTGGGTCCAAACAAGTTGAAATAG

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|125054197|gb|EL125011.1|EL125011
EST:     ATCAGCATCAGAAGCTAGAAAAGCTTTACATATCCACTCGTGCTGCTAAG                         CATTACCAAAGAGA
genomic: ATCAGCATCAGAAGCTAGAAAAGCTTTACATATCCACTCGTGCTGCTAAGgttgtttttc ... tcgttttcagCATTACCAAAGAGA
EST: gi|47831064|gb|CK120748.1|CK120748
EST:     ATCAGCATCAGAAGCTAGAAAAGCTTTACATATCCACTCGTGCTGCTAAG                         CATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGG
genomic: ATCAGCATCAGAAGCTAGAAAAGCTTTACATATCCACTCGTGCTGCTAAGgttgtttttc ... tcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttgaagttttgattactattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG
                    tattgat  putative branch site (score: 3)
                                     ttcgttcttcgttttc  putative PPT
               attactattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtttttcttaagcttttgactagtttgaagttttgattactattgattttggactcattcgttcttcgttttcagCATTACCAAAGAGATATTGTTCGTGGTGTGGAAGGTTATATAGTTACAGGGTCAAAACAAGTTGAAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG