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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttttataccatcctcagcattcttgtattggaaatggaagtttaagatttgcagaaactcttccgacaattgctattgtatgtag

Basic information

species Arabidopsis thaliana
transcript AT1G17370.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 6
GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagtttt--ttataccatc-ctcagca-------ttcttgtattggaaatggaagtttaagatttgcagaaactcttccgacaattgctattgtatgtag---------------------------------------------------------------------------------------------------
|||||| ||||||||||||||| ||| | ||||| |||||||||||||| | | ||||| | ||||| |||||||| || | ||| ||||||||||   |   |  ||  || || |         | | | |    | | | |||||  || ||| |  || |||     ||      || | |   |                                                                                                    
GTCACTACAATATATTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGTTGTTTGCATGCTTTTCTGTCTATCCCAGTTGTTCgtaagtttcactctcatgatttcttagtaaaacagtcgcctctttctttatttgtagtttcggacttgaatcaa-tctctgttcatccaaaatggaaaaaaaaattgtactgtctcaaaggatagttgtacggtatgttctttgcaattatgttggtaacttagattggctcatcatatttattttttctggcggctccag

upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 6
GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagtt----ttttataccatcct-------cagcattcttgtattggaaatggaagtttaagatttgcagaaactcttccgacaattgctattgtatgtag
|||| | ||| || |||||||| ||| | ||||| |||||||||||||| | ||||||| | ||||| |||||||| || ||||| |||||||||    | | ||    || |       |||   ||   | |  | | | | |||||  || ||| |  ||    ||     || |  | |  |   | 
GTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTCgtaagtttcactctcatgatttcttagtaaagcagtcatccactttctgtatttggagttttggacttgaaccaatc--tctattcatcgaaaatagaaaaa-
















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|124751785|gb|EH841915.1|EH841915
EST:     TGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
genomic: TGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
EST: gi|116486725|gb|EG529317.1|EG529317
EST:     GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGCCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
genomic: GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
EST: gi|116386087|gb|EG428679.1|EG428679
EST:     GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
genomic: GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
EST: gi|116486731|gb|EG529323.1|EG529323
EST:     GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
genomic: GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
EST: gi|125300199|gb|EL314284.1|EL314284
EST:     TGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAAGAAAACTGGGCGTTCAAGAGGTATTT
genomic: TGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCA-GAAAACTGGGCGTTCAAGAGG-ATTT
EST: gi|125113806|gb|EL164490.1|EL164490
EST:     TGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAAGAAAACTGGGCGTTCAAGAGGATTTG
genomic: TGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCA-GAAAACTGGGCGTTCAAGAGGATTTG
EST: gi|124919113|gb|EH992893.1|EH992893
EST:     TGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAAAGAAAACTGGGCGTTCAAGAGGATTT
genomic: TGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCA--GAAAACTGGGCGTTCAAGAGGATTT
EST: gi|116486728|gb|EG529320.1|EG529320
EST:     GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
genomic: GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
EST: gi|116386137|gb|EG428729.1|EG428729
EST:     GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
genomic: GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
EST: gi|164053578|gb|ES118712.1|ES118712
EST:     TACTGATGCAATGTCTTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTC
genomic: TACTGATGCAATG-C-TGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTC
EST: gi|116477129|gb|EG519721.1|EG519721
EST:     GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTC                         GGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG
genomic: GTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttt ... ttgtatgtagGGATGCAAGAGTTATGTGGGATCAGAAAACTGGGCGTTCAAGAGGATTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCACTTCAATATATTTGTTGGGGATTTGAGTCCGGAGGTTACTGATGCAATGCTGTTTACTTGCTTCTCTGTCTACCCGACTTGCTCgtaagttttttataccatcctcagcattcttgtattggaaatggaagtttaagatttgcagaaactcttccgacaattgctattgtatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT