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

CGATGTTGTTGAGCCAATCCTCCTTGAGGTCGATCAGATTTACCATTTAGCTTGTCCAGCTTCACCTGTTCATTACAAGTATAATCCAGTCAAGACTATCatatccttttgattacgggtcgtgatttgcaagttctgattctaaatccgttatacaaatttaggcaacattaggttggtgatcattgttattagcatcc...

Basic information

species Arabidopsis thaliana
transcript AT3G53520.1
intron # 1
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53520.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G370048_T01 (Zea mays), 5'ss of exon 2
CGATGTTGTTGAGCCAATCCTCCTTGAGGTCGATCAGATTTACCATTTAGCTTGTCCAGCTTCACCTGTTCATTACAAGTATAATCCAGTCAAGACTATCatatccttt-tgattacgggtcgtgatttgcaagttctgattctaaatccg--ttatacaaatttaggcaacattaggttgg-tgatcattgttattagcatcc
|||||| || || ||||||||||| |||||||| | ||| |||||  | || || || || || || ||||||||||||||||| ||| ||||||| |||||||||||   || |     || |   |||    | || |   | ||  ||  || | ||  | |   ||   ||   |||| ||      |    | |     
CGATGTAGTCGAACCAATCCTCCTCGAGGTCGACCGGATCTACCACCTCGCATGCCCCGCGTCGCCCGTTCATTACAAGTATAACCCAATCAAGACGATCatatccttcacgactggatctcatcggttgattttgcttacattgaaagcgacttgttcacctgttttcattttttttttgggtgggtggcgg-gctggtt---

upper sequence: AT3G53520.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 5'ss of exon 2
CGATGTTGTTGAGCCAATCCTCCTTGAGGTCGATCAGATTTACCATTTAGCTTGTCCAGCTTCACCTGTTCATTACAAGTATAATCCAGTCAAGACTATCatatcctt-ttgattacgggtcgtgatttgcaagttctgattctaaatccgttatacaaatttaggca---acattaggttggtgatcatt--gttat-tagcatcc-----------
                || ||  | ||||| |||||||| || || || ||||| || ||||| || |||||||||||||||||||| || || || || |||||||| ||||||       ||   |||||| || ||||| |   |  ||| |      ||           ||   || |    | ||  ||| | | | |  |           
---------------GATACTGTTGGAGGTGGATCAGATCTATCACTTGGCTTGCCCTGCTTCCCCAGTTCATTACAAGTATAATCCTGTTAAAACAATTATATCCTTATTGATTgtta--tgttggttgcaaattttgatt-tgggtttgttgtgtgcgattgcctttttgtcttgtcttagcctccgtttagttgtctggaaaactgaggaagaga

upper sequence: AT3G53520.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S60_124V6.1 (Physcomitrella patens), 5'ss of exon 1
CGATGTTGTTGAGCCAATCCTCCTTGAGGTCGATCAGATTTACCATTTAGCTTGTCCAGCTTCACCTGTTCATTACAAGTATAATCCAGTCAAGACTATCatatccttttgattacgggtcgtgatttgcaagttctgattcta---aatccgttatacaaatttaggcaacattaggttggtgatcattgttattagcatcc
||| || || |||||  || | || |||||||||||||| |||||  | ||||| || || |||||||| || |||||||  || || |||||||| |||||||||||||     |    |   | |||    |   | ||      ||   | |   || | ||   ||       | || ||    ||  | || |   | 
CGACGTCGTGGAGCCTCTCTTGCTGGAGGTCGATCAGATCTACCACCTTGCTTGCCCTGCCTCACCTGTCCACTACAAGTTCAACCCTGTCAAGACAATCatatccttttccaccctctcctccagttgatgatcacgttttcgcacaaaatgcttgtcagactttatcagagcgtagctgttg--tgtttctgtt-gtgcct

upper sequence: AT3G53520.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S120_29V6.1 (Physcomitrella patens), 5'ss of exon 1
CGATGTTGTTGAGCCAATCCTCCTTGAGGTCGATCAGATTTACCATTTAGCTTGTCCAGCTTCACCTGTTCATTACAAGTATAATCCAGTCAAGACTATCatatccttttgattacggg-tcgtga-----tttgcaagttctgattctaaat----ccgttataca-aatttaggcaacattaggttggtgatcattgttat-tagcatcc------------------
             ||  |  | || ||||| || |||||||||||| | || ||||| || || || || |||||||| |  |||||| |||||||||||||||||||||   | |||| || |||     ||   || |  ||| | ||  |       || | || | |      | ||    |   ||   | | ||  |  ||| |||                  
------------ACCCCTGTTGCTGGAGGTGGACCAGATTTACCATCTGGCATGTCCGGCGTCGCCCGTGCATTACAAATTCAATCCAATCAAGACTATCATATCCTTTTTTgttcgggatcttgaatttattctgaattattgagtttatgtagtgttattttgcatagtccttctagcagagagaatgtatccgtggtcgtgcagcctccttgacctgcctccacaag

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|164164061|gb|ES117232.1|ES117232
EST:     CTTGTCCAGCTTCACCTGTTCATTACAAGTATAATCCAGTCAAGACTATC                         AAGACAAATGTTAATTGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGA
genomic: CTTGTCCAGCTTCACCTGTTCATTACAAGTATAATCCAGTCAAGACTATCatatcctttt ... atagttttacAAGACAAATGT-AAT-GGGCACTCTCAATATGTTGGGTCTTGCAAAGAGA