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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatcttttaacagcgatagattattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA

Basic information

species Arabidopsis thaliana
transcript AT5G13300.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------------gtatgctagttcaaattttcacagctaattaggattgtag-ctctacatt-tagagttttcttctggctgaaacat--gtatcttttaacagcgatagattattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
                                                                                  |   | ||    | | | | |   ||  |  ||||    ||||| ||| |    |  || | | ||| |  | |   |||||   |  |   | | || ||  || ||| |||||||||||||||||| || ||||| ||||| || ||||| || |||||| |||| ||| ||||||| || || |||||||||||||| ||||| |||||||||
gtaagtggtaacttagtctgcagttttagacttacaaaaaccaaaagtttgtttgctcatttatttgcaaattctgttggaaaatatggtctggactctta-actcaagaaccattgggctctctatattcttctctcctcgttttgcttatgctttgctatctagcattaaaaacatat-atgtttgcttattacagTGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTTGCAAGTTCACTGGAAGCATTTGGAGGGGGGCATAATGATCCAATCAGTGTTGCTTTTGGA

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 2
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatcttttaacagcgatagattat-tctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
                || ||   |    |   ||| ||   | | |||||    |   ||   ||  |        | |        |  ||  |||  | |  |||||| ||| |||||| |||| || || || ||||| || ||||| || |||||  |||| ||||||||||| |||||||| ||||| || |||||||| |||||||| 
--------------cattgcattacacgcttatatt-taaacccatatttactcgtagttttctgccaacttgctgctatccaggacacattaatttacatatcccttttttcagGGAAGGATTAGGAGAAGCTTATGATGGAGATATTGCATTTGCAAGCTCACTCGAAACATTTGGGGGAGGCCACAATGACCCTATAAGTGTTGCTTTTGGT

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 2
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatcttttaacagcgatagattattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
    |  |||  ||   | ||  ||  ||  | ||| ||  |    ||   |||| |  ||   |||| ||       | |    ||      ||| || |  | || || ||||||||||||||| || ||||||||||| || ||||| || || ||  |||||||||||||||| |||||||| ||||||||||| ||||| |||||||| 
----gtaagt--aaccatccattgcccat--gcatt-tattttgtaatccggagtatggttg-agctgtaagtcactccctgcgccatatgctgat-atgcccttttgtttcagTGAAGGACTAGGGGAAGCATACGATGGAGATATTGCATTTGCCAGCTCACTTGAAACATTTGGAGGAGGCCACAATGATCCAATGAGTGTCGCTTTTGGT

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 2
--gtatgctagt-tcaaattttcacagctaattaggattgt---agctctacatttagagttttcttctggctgaaacat-------gtatcttttaacagcgatagattattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
     || || | |   |||| |  |||  ||| || ||     | |   | | ||     | |  | ||    ||   |       |  | | |  |   |  |  | | |    | || || ||| ||||||||||| || ||||| ||||| || ||||| ||||||||  |||||||||||||||| || || |||||||||||||| |||||  | ||||||
gtaagtgataatgtgtcatttacgtagcatatttgggttaccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctatgcctttctaatttctacttttgtttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatcttttaacagcgataga-----ttattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
               || |||||||| || |  ||        |  || | || |||     ||   || |  | | |  ||||   ||  ||       | | | ||    ||| |||||||||||| || ||||| || ||||| || ||||| || ||||||||  | ||||| |||||||| || |||||||| ||||| |||||||||||||||
---------------ttctcacagcttatcataat----atattgaatattgattttgaagatgttagatatgtattttctttataggctttatttgctttcacttttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatctttta---acagcgatagattattctttct-ttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
               || |||||||| || |  |         |  || | || |||     ||   || |  | | |  ||||   ||    || | ||   |||| |  ||| |||||||||||| || ||||| || ||||| || ||||| || ||||||||  | ||||| |||||||| || |||||||| ||||| |||||||||||||||
--------------tttctcacagcttatcataac----atattgaatattgattttgaagatgttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 2
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatcttttaacagcgatagattattctttcttt-ttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
   || || ||||   |||    | |  ||| |  || |  || ||||||     ||||  |       | ||||  | |  |     | || |  | |  | |||   || ||||||||| || || || | ||| ||||||||||||||||| |||||||| || ||||| ||||||||||| || |||||||| || |||||||||||||||
--ttgtta-ttcag--ttttggtgtttcttatggatg-aaatcaacattt----ctttccac-----atagcatgcttgtcatggtttcaattgtctctgttctctgaattgcagTGAAGGGCTTGGGGAAGGATATGATGGGGACATTGCTTTTGCAAGTGCTCTAGAAACTTTTGGTGGAGGACACAATGATCCTATTAGTGTGGCTTTTGGA

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ24732 (Selaginella moellendorffii), 3'ss of exon 2
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatcttttaacagcgatagattattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
                                    |||   | || ||||  |  |  || ||       |||||    |    | |   | | || |  ||| ||  |||||||||||||| || || || |||||||| || || ||||| || |||||  | |||||||||||||| || ||| ||||||| || || || ||| |||||
------------------------------------gtaagcccac-tttaccgagtaattgtgttc----catgttcaatc---cggtctttgtttctctttttttcctacagTGAAGGACTCGGTGAAGCGTACGATGGAGATATCGCTTTTGCTAGTGCTTTGGAAACATTTGGTGGCGGGCATGATGATCCCATTAGCGTCGCTGTTGGA

upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ08060 (Selaginella moellendorffii), 3'ss of exon 2
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatcttttaacagcgatagattattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
                                    |||   | || | ||  |  |   | ||       |||||    |    | |   | | || |  ||| ||  |||||||||||||| || || || |||||||| || || ||||| || |||||  | |||||||||||||| || ||| ||||||| || || || ||| |||||
------------------------------------gtaagcccac-tctaccgagtaactgtgttc----catgttcaatc---cggtctttgtttctctttttttcctacagTGAAGGACTCGGTGAAGCGTACGATGGAGATATCGCTTTTGCCAGTGCTTTGGAAACATTTGGTGGCGGGCATGATGATCCCATTAGCGTCGCTGTTGGA

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|19877169|gb|AU238000.1|AU238000
EST:     ATATTGCGGGAAAGAAGTCTCAAGTTTTACAAAGGATGCCGGAAATACAC                         TGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACT
genomic: ATATTGCGGGAAAGAAGTCTCAAGTTTTACAAAGGATGCCGGAAATACACgtatgctagt ... ctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctggctgaaacatgtatcttttaacagcgatagattattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA
                    ttttaac  putative branch site (score: 2)
                                    ttattctttcttttta  putative PPT
                               atagattattctttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctagttcaaattttcacagctaattaggattgtagctctacatttagagttttcttctggctgaaacatgtatcttttaacagcgatagattattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG