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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctgcttatatccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagttgtgttgtgccgttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACACCAACCAG

Basic information

species Arabidopsis thaliana
transcript AT3G06680.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06680.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1
------gttagctgctt-atatccggctgatcgctggatataa-tttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagttgtgttgtgccgttg-------ttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACACCAACCAG
      |     | ||  || |||  |   ||  | ||| |   ||||| || |   |||||   ||| || |  || |   ||| |||      ||||     | | |||            || ||||| || |||||||| |||||||||||||| |||||   ||||||||| |||||||| ||||||||||| | | | ||||| || |          
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgt-tttcttcccctgattcctgatttttttcgtttgttcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA----------

upper sequence: AT3G06680.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
gttagctgcttata-tccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaag--ttgtgtt-gtgccgttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACACCAACCAG
|| |    |    | ||||   ||||  |   ||  |  ||  || |   ||||| |  |   | |         | | | |||   |  || |||| |    | |     ||| ||||| || |||||||| |||||||||||||| |||||   ||||||||| |||||||| ||||||||||| | | | ||||| ||            
gtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----------

upper sequence: AT3G06680.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147791_T01 (Zea mays), 3'ss of exon 1
gttagctgcttatatccggct-gatcgctggata--taatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaa--aagttgtgttgtgccgttgtt--acagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACACCAACCAG
|| |    |    | || ||| |||| |    ||     | ||| |||   ||   | |||              | | | | |||       | ||||| || |   |     ||||||||| || |||||||| |||||||||||||| |||||   ||||||||| |||||||| || ||||| || | | | ||||| ||            
gtaattctcaggcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcac-cgtcaacccacccctccacttactctgattcgcactttgttg-gcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------

upper sequence: AT3G06680.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147791_T02 (Zea mays), 3'ss of exon 1
gttagctgcttatatccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagttgtgttgtgccgttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACACCAACCAG
                               | | ||||   | || ||  |   |        |     | | |  | ||   |  ||||     | | |    | ||||||||| || |||||||| |||||||||||||| |||||   ||||||||| |||||||| || ||||| || | | | ||||| ||            
------------------------------gtgtgattttcgtcttcaccgtcaac--ccacccctccacttactctgattcgcactttgttggcagGCATCCGGA-AGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------

upper sequence: AT3G06680.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 1
gttagctgctt-atatccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagttgtgttgtgccgttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACACCAACCAG
|    | |||  || ||   || |||| ||    | ||||   | || ||  |   |        |     | | |  | ||   |  ||||     | | |    | ||||||||| || |||||||| |||||||||||||| |||||   ||||||||| |||||||| || ||||| || | | | ||||| ||            
gcaccccgctcgatctcatcctaatcggtg----tgattttcgtcttcaccgtcaac--ccacccctccacttactctgattcgcactttgttggcagGCATCCGGA-AGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------

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|164019424|gb|ES108560.1|ES108560
EST:     GTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAG                         AAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTC
genomic: GTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAGgttagctgct ... gttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTC
EST: gi|86078453|gb|DR374210.1|DR374210
EST:     ACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAG                         AAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGC
genomic: ACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAGgttagctgct ... gttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGC
EST: gi|164182526|gb|ES127859.1|ES127859
EST:     TGTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAG                         AAATGGCGAAATCGAAGAATCACACGGCGCAC
genomic: TGTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAGgttagctgct ... gttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCAC
EST: gi|125165114|gb|EL191543.1|EL191543
EST:     ACCTANCTTTCCTCTCGCGTCTCTCCCCTTTACTCAG                         AAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGT
genomic: ACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAGgttagctgct ... gttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGT
EST: gi|164158131|gb|ES107672.1|ES107672
EST:     TGTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTAACTCAG                         AAATGGCGAAATCGAAGAATCACACGGCGC
genomic: TGTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTA-CTCAGgttagctgct ... gttgttacagAAATGGCGAAATCGAAGAATCACACGGCGC
EST: gi|164096352|gb|ES200129.1|ES200129
EST:     TGTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAG                         AAATGGCGAAATCGAAGAATCACACGGCGC
genomic: TGTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAGgttagctgct ... gttgttacagAAATGGCGAAATCGAAGAATCACACGGCGC
EST: gi|152034411|gb|BP827764.2|BP827764
EST:     TCACCTATCTTT-CTCTCGCGTCTCTCCCCTTTACTCAG                         AAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGC
genomic: TCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAGgttagctgct ... gttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGC
EST: gi|164067799|gb|ES216358.1|ES216358
EST:     GTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAG                         AAATGGCGAAATCGAAGAATCACACGGCGCA
genomic: GTCACCTATCTTTCCTCTCGCGTCTCTCCCCTTTACTCAGgttagctgct ... gttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtttgtttcgttggtgattgagtttgaaaagttgtgttgtgccgttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACACCAACCAG
                        tttgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagctgcttatatccggctgatcgctggatataatttgacttttaactcttctcgtttgtttcgttggtgattgagtttgaaaagttgtgttgtgccgttgttacagAAATGGCGAAATCGAAGAATCACACGGCGCACAATCAGTCTGCCAAGGCGCATAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACACCAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA