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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtcccttacctaactccttcaatgatcacatagcgataatgttgctaatttcgaagcccttacacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA

Basic information

species Arabidopsis thaliana
transcript AT2G33340.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G33340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 15
-------------gtaaagtcccttacctaactccttcaatgatcacatagcgataatgttgctaatttcgaagccct----tacacttg---cagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA
              ||  | ||     ||   | | | | ||    |   ||    |  |  ||||||| |   |  |    |||||||    |||| ||||  ||    || ||||||||  | |||||  ||||| |||| || ||||| ||||| |||||||||||||||||||| | ||| || || ||  |
gttcgtccctttcttatggcccacattctcggttcgtgattggcatctgtgcttgcacttaactaatttggtttctgtggcgtacacttttctcagGGAAAGTGACAAACGTCAAGTTTGGCACCGATGCGAAGTACATTGCCGTAGGTTCTATGGATCGTAACCTACGGATATTTGGGCATCCGGGAGAAGATGA

upper sequence: AT2G33340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G324540_T01 (Zea mays), 3'ss of exon 17
-----------------gtaaagtccctta-cctaactccttcaatgatcacatagcgataatgttgctaatttcgaagcccttacactt--gcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA
                   | |||| |||     || | ||||   | ||    ||||   ||     |  | | |   |  ||   |||   |||| ||||  || |  || || || ||   ||| ||  | ||| | ||  | ||||| |||||||| || ||||||||||||||||| ||||| |||||  |
gtgtgtccctctttttaccatagtctcttggtgcaatttcttcttagttcttggagcgcacattgacttggtgttgtgacatttgtccttccacagGGAAAGTAACTTCCGTAAAATTCGGAGTAGACGCGAAATACATAGCCATAGGTTCTATGGACCGCAATCTACGGATATTTGGTCTCCCTGGAGATGATCA

upper sequence: AT2G33340.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G324540_T02 (Zea mays), 3'ss of exon 16
----------------------------------------gtaaagtccctta-cctaactccttcaatgatcacatagcgataatgttgctaatttcgaagcccttacactt--gcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA-----------------------
                                          | |||| |||     || | ||||   | ||    ||||   ||     |  | | |   |  ||   |||   |||| ||||  || |  || || || ||   ||| ||  | ||| | ||  | ||||| |||||||| || ||||||||||||||||| ||||| |||||  |                       
attacccgatttatcaggaacaggtgtgtccctctttttaccatagtctcttggtgcaatttcttcttagttcttggagcgcacattgacttggtgttgtgacatttgtccttccacagggaaagtaacttccgtaaaattcGGAGTAGACGCGAAATACATAGCCATAGGTTCTATGGACCGCAATCTACGGATATTTGGTCTCCCTGGAGATGATCAAATGGAGGAATCAAACACAGCGG

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|116472804|gb|EG515396.1|EG515396
EST:     GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTTTCCGGCACTG                         GTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
genomic: GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTCTCCGGCACTGgtaaagtccc ... acacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
EST: gi|86059718|gb|DR355475.1|DR355475
EST:     TCCCAGATCTCTCCGGCACTG                         GTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
genomic: TCCCAGATCTCTCCGGCACTGgtaaagtccc ... acacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
EST: gi|116444557|gb|EG487149.1|EG487149
EST:     GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTCTCCGGCACTG                         GTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
genomic: GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTCTCCGGCACTGgtaaagtccc ... acacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
EST: gi|124953130|gb|EL028347.1|EL028347
EST:     CTCCGGCACTG                         GTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
genomic: CTCCGGCACTGgtaaagtccc ... acacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCG
EST: gi|124955811|gb|EL030793.1|EL030793
EST:     GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGNTCTCTCCGGCACTG                         GTAAAGCTACGTG
genomic: GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTCTCCGGCACTGgtaaagtccc ... acacttgcagGTAAAGCTACGTG
EST: gi|124731446|gb|EH822848.1|EH822848
EST:     GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTCTCCGGCACTG                         GTAAAGCTACGTGTGTGAAGTTTGGTT
genomic: GAAAGCTGAATGGAACCTTATCAAGACACTCCCAGATCTCTCCGGCACTGgtaaagtccc ... acacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaatgatcacatagcgataatgttgctaatttcgaagcccttacacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA
                                        cccttac  CT-rich tract
                   ataatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtcccttacctaactccttcaatgatcacatagcgataatgttgctaatttcgaagcccttacacttgcagGTAAAGCTACGTGTGTGAAGTTTGGTTCAGATGCACAGTACGTTGCAGTCGGTTCGATGGACCGTAACCTACGGATATTTGGTCTTCCTGGTGATGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA