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

AGTCTGATGATCCAGTGCTGGATAGAATTGCCCGGTTCCAAAATGCTTGCTGGAGATTTCTTAGACCCCATACAATCCGCGGAACAGCTTTAGGATCCACgtcagtatttttgttgcatatttatttatgaagaacttgatagtttctgctctcatttatcttgactgtaattttaatggcag

Basic information

species Arabidopsis thaliana
transcript AT3G11945.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11945.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G113476_T03 (Zea mays), 5'ss of exon 2
AGTCTGATGATCCAGTGCTGGATAGAATTGCCCGGTTCCAAA-ATGCTTGCTGGAGATTTCTTAGACCCCATACAATCCGCGGAACAGCTTTAGGATCCACgtcagtatttt-tgttgcat-atttatttatgaagaacttgatagtttctgctctcatttatcttgac----tgtaattttaatggcag-----------
  |         |  |  |  |    | ||   |    |||  || | |||||||||||| | || || ||||||||||| ||||| ||||||||||||| || ||| | |  || |  || |||||  | |  |      | ||  || | ||  |  |   |   |     || |||| ||    ||            
-CTGGAGCAGCTCCATTATCAAAGACACTGTTAGACCTCAAGGATTCCTGCTGGAGATTTTTAAGGCCACATACAATCCGAGGAACTGCTTTAGGATCCATgtgagtttctaatgctctattatttagatttataatgtcagctacgttgtactacctctgtccacaaaataatgcaattctaggtacattcttggtcaac

upper sequence: AT3G11945.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv08s0007g07200.t01 (Vitis vinifera), 5'ss of exon 2
AGTCTGA---TGATCCAGTGCTGGATAGAATTGCCCGGTTCCAAAATGCTTGCTGGAGATTTCTTAGACCCCATACAATCCGCGGAACAGCTTTAGGATCCACgtcagtatttttgttgc--atatttatttatgaagaacttgatagtttctgctctcatttatcttgactgtaatt-ttaatggcag-----------------------
   |||    |||||||   ||| | | | || |   |||| || |||| |||||||||||  | ||||||||||| || ||||||||||| ||||| ||||||| |||| |  |  |||  || || | |||| ||    || || | | ||| || ||   ||  || ||  |||| || |   | |                       
---CTGGATCTGATCCACCACTGAACAAATTTTCAGTGTTCAAAGATGCATGCTGGAGATTCTTAAGACCCCATACGATTCGCGGAACAGCATTAGGGTCCACgtaagtaataatcatgctaatcttgagttattaatggttt-attgatcctgatcccaag-attatgcctagaattcttgacttcggttcatcttttcttcttttgacag
















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|124833942|gb|EH918381.1|EH918381
EST:     TCCGCGGAACAGCTTTAGGATCCAC                         TGCCTTGGTGACAAGAGCTTTGATAGAGAACACTCATTTGATCAAATGGAG
genomic: TCCGCGGAACAGCTTTAGGATCCACgtcagtattt ... ttaatggcagTGCCTTGGTGACAAGAGCTTTGATAGAGAACACTCATTTGATCAAATGGAG
EST: gi|124770327|gb|EH860457.1|EH860457
EST:     TGGAGATTTCTTAGACCCCATACAATCCGCGGAACAGCTTTAGGATCCAC                         TGCCTTGGTGA
genomic: TGGAGATTTCTTAGACCCCATACAATCCGCGGAACAGCTTTAGGATCCACgtcagtattt ... ttaatggcagTGCCTTGGTGA
EST: gi|86085149|gb|DR380908.1|DR380908
EST:     TGGAGATTTCTTAGACCCCATACAATCCGCGGAACAGCTTTAGGATCCAC                         TGCCTTGGTGACAAGAGCTTTGATAGAGAACACTCATTTGATCAAATGGAG
genomic: TGGAGATTTCTTAGACCCCATACAATCCGCGGAACAGCTTTAGGATCCACgtcagtattt ... ttaatggcagTGCCTTGGTGACAAGAGCTTTGATAGAGAACACTCATTTGATCAAATGGAG
EST: gi|125073376|gb|EL137732.1|EL137732
EST:     AACAGCTTTAGGATCCAC                         TGCCTTGGTGACAAGAGCTTTGATAGAGAACACTCATTTGATCAAATGGAG
genomic: AACAGCTTTAGGATCCACgtcagtattt ... ttaatggcagTGCCTTGGTGACAAGAGCTTTGATAGAGAACACTCATTTGATCAAATGGAG
EST: gi|124916881|gb|EH990755.1|EH990755
EST:     CAGCTTTAGGATCCAC                         TGCCTTGGTGACAAGAGCTTTGATAGAGAACACTCATTTGATCAAATGGAG
genomic: CAGCTTTAGGATCCACgtcagtattt ... ttaatggcagTGCCTTGGTGACAAGAGCTTTGATAGAGAACACTCATTTGATCAAATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCTGATGATCCAGTGCTGGATAGAATTGCCCGGTTCCAAAATGCTTGCTGGAGATTTCTTAGACCCCATACAATCCGCGGAACAGCTTTAGGATCCACgtcagtatttttgttgcatatttatttatgaagaacttgatagtttctgctctcatttatcttgactgtaattttaatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT