Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttatttggtttccaacacaacttttgcaaacagagttatgtatttacattttgtgctttgtttatatatcgggtgctctgtctctgctgcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTCATATGTGGCTTGTTTTACGCCGCTTGAAGGAAGATGGACAGGAAGGTGT

Basic information

species Arabidopsis thaliana
transcript AT5G51220.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G51220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g30790.1 (Oryza sativa), 3'ss of exon 2
-----gtactttatttggtttccaacacaacttttgcaaacagagttatgtatttacattttgtgctttgtttatatatcgggtgctctgtctctgctgcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTCATATGTGGCTTGTTTTACGCCGCTTGAAGGAAGATGGACAGGAAGGTGT
           ||  || |||   |      | || ||     |  | | |||    |   | | ||  ||    |  |    ||   | |  ||  | |||| ||  | |||||||||||||| |||| ||| | |||  | ||||| || |||||||||||| || |||| |||||||| ||||| ||  |||| |||||
cattaactgcatacctgttttggtaactgtttgtttcatttccatctttttatgcttaagatatactgggtcggcaatttc--tgacattttccttttacagTTTTTCAGTTGGAGAAAACATTTAAAACAACATTTTCATTACTTGTTCTCCATATGTGGCTTATTCTACGTCGCTTGAAAGAAGAAGGGAAGGATGGTGT

upper sequence: AT5G51220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G06170.1 (Glycine max), 3'ss of exon 2
gtactttatttggtttccaacacaacttttgcaaacagagttatgtattta--cattttgtgctttgtttatatatcgggtgctctgtctctgct-gcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTCATATGTGGCTTGTTTTACGCCGCTTGAAGGAAGATGGACAGGAAGGTGT
 |    || |     |     |  | |||       |    |    ||  |   | | | || | |  |   ||           |   |||||| ||||| || |||||||||||||||||||||| ||| |  ||  | ||||| |||||||||||| |   ||| || ||||||||| |||| ||| |||| |||||
atcgagtaatcatggtatgggaggagtttgatttgtattactgctcatcaaactagtgtttgatcttgtagcattctaaacttcttccttctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTCATATGTGGTTCTGTTTGCGTCGCTTGAAGCAAGAGGGAAAGGAGGGTGT

upper sequence: AT5G51220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0013g01540.t01 (Vitis vinifera), 3'ss of exon 4
---------gtactttatttggtttccaacacaacttttgcaaacagagttatgtatttacattttgtgctttgtttatatatcgggtgctctgtctctgctgcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTCATATGTGGCTTGTTTTACGCCGCTTGAAGGAAGATGGACAGGAAGGTGT
         |    | ||||| | |   |||      || | |     | | || || |  || ||| |  |  | || |       |    | | ||   ||||| ||| |||||||||||||| || |||| ||| | ||| |||||| | |||||||||||||||   |||||||||||||| ||||||||| ||||||||||
aacaatgtagatagtgatttgttattttacatgctgctttccatgctggctttgaatctctatattg-gtctaatgtaaa-----attatattatttcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT

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|124913358|gb|EH987232.1|EH987232
EST:     GATCTACAAGCGGATCATTGCACAAGTTGATAAACCTGCAATATATGATG                         TATTCAACTTGGAGAAAACATTCAAAA
genomic: GATCTACAAGCGGATCATTGCACAAGTTGATAAACCTGCAATATATGATGgtactttatt ... tctgctgcagTATTCAACTTGGAGAAAACATTCAAAA
EST: gi|124788698|gb|EH878377.1|EH878377
EST:     AATATATGATG                         TATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTC
genomic: AATATATGATGgtactttatt ... tctgctgcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTC
EST: gi|19876603|gb|AU237434.1|AU237434
EST:     GATCTACAAGCGGATCATTGCACAAGTTGATAAACCTGCAATATATGATG                         TATTCAACTTGGAGAAAACATTCAAA-TAACGTATTCGCTGCTTGTCCTTC
genomic: GATCTACAAGCGGATCATTGCACAAGTTGATAAACCTGCAATATATGATGgtactttatt ... tctgctgcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatttacattttgtgctttgtttatatatcgggtgctctgtctctgctgcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTCATATGTGGCTTGTTTTACGCCGCTTGAAGGAAGATGGACAGGAAGGTGT
                                      ctctgtctct  CT-rich tract
                   tttgtttatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttatttggtttccaacacaacttttgcaaacagagttatgtatttacattttgtgctttgtttatatatcgggtgctctgtctctgctgcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTCATATGTGGCTTGTTTTACGCCGCTTGAAGGAAGATGGACAGGAAGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA