Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggaattttaaaattacatattttaaaaagattttgtgtctgatttatctttgctctgtatatttaagatactgatatgtagtgctgagatgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGAAGAGAGGCTAATGTTACAAAAGGCGAGAGAGCTCGACGAATTTGATCAG

Basic information

species Arabidopsis thaliana
transcript AT1G61620.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G61620.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G07150.1 (Glycine max), 3'ss of exon 1
tgggaattttaaaattacatattttaaaaagattttgtgtctgatttatctttgctctg--------tatatttaagatactgatatgtagtgctgagatgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGAAGAGAGGCTAATGTTACAAAAGGCGAGAGAGCTCGACGAATTTGATCAG
       | || | |  | |  |||| ||    ||| |   || | ||  |  | | |         ||| ||    |   | | |  |   | || ||     |||||| |||||| || ||| |  ||||  |||||||||| || || || |||||||||| | | |||||||||||||| | |||||| || | ||||||||| 
-------tctatattgtctttgtttataatatgtttttccttggtgtagataggatataatgactgttatgttgtgaaccttaaca-atgtggttgtgaataaaatagGAAGCTTGCAGCCCATGCTGCTCAGCAGAAGCAAGAAAAAGAGGAGGAAGAAGAGAAGTTGATGTTACAAAAGGCTAAAGAGCTTGATGCATTTGATCAA
















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|86041758|gb|DR337513.1|DR337513
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041751|gb|DR337506.1|DR337506
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041746|gb|DR337501.1|DR337501
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041770|gb|DR337525.1|DR337525
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041768|gb|DR337523.1|DR337523
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041757|gb|DR337512.1|DR337512
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041753|gb|DR337508.1|DR337508
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041750|gb|DR337505.1|DR337505
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTGCAAAAGAAGCAAGATAAGGATGAAGAAG
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCT-CAAAAGAAGCAAGATAAGGATGAAGAAG
EST: gi|86041767|gb|DR337522.1|DR337522
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041745|gb|DR337500.1|DR337500
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041765|gb|DR337520.1|DR337520
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041756|gb|DR337511.1|DR337511
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041749|gb|DR337504.1|DR337504
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041763|gb|DR337518.1|DR337518
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041762|gb|DR337517.1|DR337517
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|19877147|gb|AU237978.1|AU237978
EST:     AGAGAGTGTATGCTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041748|gb|DR337503.1|DR337503
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041771|gb|DR337526.1|DR337526
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|124815623|gb|EH900489.1|EH900489
EST:     AAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041752|gb|DR337507.1|DR337507
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041769|gb|DR337524.1|DR337524
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041755|gb|DR337510.1|DR337510
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041754|gb|DR337509.1|DR337509
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041764|gb|DR337519.1|DR337519
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041747|gb|DR337502.1|DR337502
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
EST: gi|86041759|gb|DR337514.1|DR337514
EST:     AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAG                         GAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA
genomic: AGAGAGTGTATACTTGAATGTTTCCTTGCTCAGAAGAAAGATATCCAAAGgtataaactt ... atgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctttgctctgtatatttaagatactgatatgtagtgctgagatgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGAAGAGAGGCTAATGTTACAAAAGGCGAGAGAGCTCGACGAATTTGATCAG
                         tactgat  putative branch site (score: 2)
            tgtatatttaagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggaattttaaaattacatattttaaaaagattttgtgtctgatttatctttgctctgtatatttaagatactgatatgtagtgctgagatgtctatagGAGGCTTGCTGCACATTCGTCTCAAAAGAAGCAAGATAAGGATGAAGAAGAAGAGAGGCTAATGTTACAAAAGGCGAGAGAGCTCGACGAATTTGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - -aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagatac