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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaattcaattagttgactgtttttttttctatctttttctgagtgaggtttcattgatttgtttgtttgttccccttcaaattacaagGTTGAGCTTCAAACAGTAGATGGATTGGTAAAAGACAGTACACAGTGTGCCCCAAATGGTTACTATTTCATCCCAGTATATGACAAG

Basic information

species Arabidopsis thaliana
transcript AT3G62360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G62360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g19470.1 (Oryza sativa), 3'ss of exon 2
---gtaagaattcaat--tagttgactgtttttttttctatctttttctgagtgaggtttcattgatttgttt-gtttgttccccttcaaatt----acaagGTTGAGCTTCAAACAGTAGATGGATTGGTAAAAGACAGTACACAGTGTGCCCCAAATGGTTACTATTTCATCCCAGTATATGACAAG
   ||    || || |  || || |         | |   |  |  | ||  |  ||||||  ||   || |  |  ||  || ||| |   |    |  ||||||||||    ||  | ||||| ||||| || || || || ||||||||||| ||||| |||||||| |||||||| |||||||||
cgagtcttgatgcagtgctaattcatgaccacactattctttatgctttgtatatggtttc--tgccgtgctcagactgaccctcttaactctctgaatcagGTTGAGCTGTGTACTATTGATGGTTTGGTTAAGGAAAGCACTCAGTGTGCCCCTAATGGATACTATTTTATCCCAGTCTATGACAAG

upper sequence: AT3G62360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G014788_T01 (Zea mays), 3'ss of exon 2
------gtaagaattcaattagttgactgtttttttttctatctttttctgagtgaggtttcattgatttgtttgtttgttccccttcaaatt-----acaagGTTGAGCTTCAAACAGTAGATGGATTGGTAAAAGACAGTACACAGTGTGCCCCAAATGGTTACTATTTCATCCCAGTATATGACAAG
       |     | |  |   ||   ||  | | ||| ||| ||| | |  |     || || | |         |  |||||  | || ||     |  ||||||||||    || || ||||| ||||| ||||| || ||||||||||| || ||||| |||||||| ||||| || ||||| |||
ttaatcatgcttgtgctttggttttgatgcatatgtttttatatttatttatg---atttgcactaagcctccaactgattccctcttaactttgtgtatcagGTTGAGCTCTGCACTGTTGATGGTTTGGTTAAAGAAAGCACACAGTGTGCTCCTAATGGATACTATTTTATCCCCGTCTATGATAAG

upper sequence: AT3G62360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G40520.1 (Glycine max), 3'ss of exon 2
----------gtaagaattcaattagttgactgtttttttttctatctttttctgagtgaggtttcattgatttgtttgtttgttccccttcaaattacaagGTTGAGCTTCAAACAGTAGATGGATTGGTAAAAGACAGTACACAGTGTGCCCCAAATGGTTACTATTTCATCCCAGTATATGACAAG
           ||   || |||     |  || ||| ||| | ||  | |     | |    |    |||  ||   ||    ||   |      ||  | ||||||||||||||| || |||||| ||||||| || || ||||| ||||| |||||||| |||||||| || |||||||||||||||
ggatgctgtgttacacatccaagggaattcctatttgtttat-tagatatgatgcactcgtttcaacttggattcaatgacaattgatccatttgttgta-gGTTGAGCTTCAAACTGTGGATGGACTGGTAAAGGATAGAACACAATGTGCTCCAAATGGATACTATTTTATTCCAGTATATGACAAG

upper sequence: AT3G62360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G37930.2 (Glycine max), 3'ss of exon 2
-gtaaga-attcaattagttgactgtttttttttctatctttttctgagtgaggtttcattgattt--gtttgtttgttccccttca--aattaca--agGTTGAGCTTCAAACAGTAGATGGATTGGTAAAAGACAGTACACAGTGTGCCCCAAATGGTTACTATTTCATCCCAGTATATGACAAG
 | | ||   |   |||     |        || || | | ||| | ||  | | | || |  |||    || |   |  |  || |  | ||     |||||||||||||||| || |||||| ||||||| || || ||||| ||||| || ||||| |||||||| || |||||||||||||||
aggaggatgctgtgttacacatccaagggaattcctgtttgtttattaggtatgatgcacttgtttcaacttttcaatgacaattgatcatttgttgtagGTTGAGCTTCAAACTGTGGATGGACTGGTAAAGGATAGAACACAATGTGCTCCCAATGGATACTATTTTATTCCAGTATATGACAAG

upper sequence: AT3G62360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0005g01650.t01 (Vitis vinifera), 3'ss of exon 2
----------gtaagaattcaattagttgactgtttttttttctatctttttctgagtgaggtttcattgatttgtttgtttgttcccctt--caaattacaagGTTGAGCTTCAAACAGTAGATGGATTGGTAAAAGACAGTACACAGTGTGCCCCAAATGGTTACTATTTCATCCCAGTATATGACAAG
             |  ||||   | ||| | || |  ||||    |  |       |     ||  |||||  |  |   | |||    ||  |||| |  | |||||||||||  ||| | ||||||||||| || ||||| || ||||||||||||||||||||||||||||| || || |||||||||
ttctatctacaccaacattc---tggttaattgctaattttgtgcttctgaaacatggatacttaaattgaggttctgaatggtttattttatcaaactgta-gGTTGAGCTTCGCACAATTGATGGATTGGTGAAGGACAGAACTCAGTGTGCCCCAAATGGTTACTATTTCATTCCTGTCTATGACAAG

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|116415210|gb|EG457802.1|EG457802
EST:     TCAGGTCTCGGAAAGGATCCGATGGGAAACCGGATTTTTCTCATATCACA                         GTTGAGCTTCAAACAGTAGATGGATTGGTAAAAGACAGTACACAGTGTGCC
genomic: TCAGGTCTCGGAAAGGATCCGATGGGAAACTGGATTTTTCTCATATCACAgtaagaattc ... aaattacaagGTTGAGCTTCAAACAGTAGATGGATTGGTAAAAGACAGTACACAGTGTGCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgagtgaggtttcattgatttgtttgtttgttccccttcaaattacaagGTTGAGCTTCAAACAGTAGATGGATTGGTAAAAGACAGTACACAGTGTGCCCCAAATGGTTACTATTTCATCCCAGTATATGACAAG
                  cattgat  putative branch site (score: 4)
                                tttgttccccttca  putative PPT
                                          ttcaaatta  TA-rich tract