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

...gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC

Basic information

species Arabidopsis thaliana
transcript AT1G10950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 1
------gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgt-caagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
       ||  |   ||| |  |     |||| |  |||| ||||     |  |  ||| || |||   | || |   ||    |||| ||| |      | | |||||  |||  || || |  || |  || ||||| |||||||| ||||| || || |||||||||||||| ||||||||| |||| ||||||||||| |  |
ctttcctaaaataaattcattattatgtttacca--taattccatgg---tagaactttgtgagctcaacagttctcatctgccttttatgcttct--tatatgcagTACAAAGTTGAAGAACCAGTTAAGCTCTGGGTGAACAAAGTCGGCCCTTACAATAATCCACAAGAAACTTACAACTATCACAGCCTTCCATTTTGTCAAC

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 1
--gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
   | || |      ||  |   || | | || |||| ||   |     || ||| | || |  |   |||  |||  |   | |   || |  || | |||||  |||| || ||   ||| |  || ||||||||||| |||||||| || || || || |||||||| |||||||||||||| || |||||||| |  |
gccatttctaaaaactaagcctactgatttgt-aatcacactgagaacaacttttgtatgttagta-atcacttcatctacctgttatttaattttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTACAATAACCCGCAAGAAACTTACAACTATTACAGCCTCCCATTTTGTCAGC

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 1
gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtc--aattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
  |||   | |   |   | | || ||  |   ||| | |  || |  ||  | ||| |  | ||   || |    ||   |||        | |  | |||||  || | || ||||  || |  || ||||| || ||||||||||| || |||||||| |||||||| |||||||| ||||| ||||||||||| |  |
-gattgctgcttgaatgttgttttccttatgcttcctacatgctgt-gcaaatatgttccgtactcaaaatttctcatccctttcaatgcttcttaatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAACAATCCTCAAGAAACTTACAACTACTACAGCCTTCCATTTTGTCAAC

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaag---tcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
   ||   | |      || | ||  |  |   ||| | |  |  |   | |  | |           |||   ||| |  ||||   | |       | |||||  || | || ||||  || |  || ||||| || ||||||||||| || || ||||| |||||||| |||||||||||||| ||||||||||| |  |
---ttgctgattgagtgctgttttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 1
gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtca-----attttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
   ||   ||  || |    | |  ||    | |    | |||| | ||  |  ||   ||  ||   || |||       || |  |   ||     | | |||||| || | || || |  || |  |||||||||||||| ||||| || || || || || |||||||| ||||||||||||||||| || ||||| |  |
---ttgctgtcttttcagaatttacctg--cactgaatttaactatgacgataatgcctttacctactaaatcattgcagcttataatatttttcttatgtgcagTATAAAACAGAAGAACCTGTTAAGCTATGGGTAAACAAGGTTGGGCCTTACAATAACCCTCAAGAAACTTACAACTATTACAGTCTCCCGTTTTGTCAAC

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 1
---------gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgcc-ttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
          |  |  | || ||||  | |  | | |   |      ||| | ||  |||   || |||||  |          ||| |  |||  ||    | ||| |||| ||||| | |||||  || || || ||||| ||||| ||||| || || |||||||| || || ||||||||||| ||||| || ||||||||||   
gcccagcgctagataggatttttacgtttt--tgccaacaagctgtctaatcgttctcatccatgcgctttctttc--------tttctgctgctgtttgtttattttagTACCAAGCAGCGGAGCCTGTGACGCTCTGGGTGAACAAGGTTGGTCCGTACAACAATCCGCAGGAGACATACAACTACTACAGCCTCCCATTTTGCCATG

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 1
----gaattt-tggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
    |||||  ||   |  | |   | |   || || ||        |       |        | |  | | ||   ||| | ||||   ||      ||||||||||||  ||| || |  || | ||| ||||| ||||||||||| || ||||||||||||||||||||||||||||||||||| || |||||||| |  |
cactgaattagtgaaacagattaaatatgtatatttcatttgtagtgccaagtggtgaacaacttctgtttttaaaagaatgtattttattttg-----tttcagTATCAACACGATGAACCAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
---gaattt-tggttcttactctctcttactagttaatcccataaacttttacatttctgtgctttt-ctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
   ||  |  ||   |  | |      |     ||    |  ||   |       |     |||| |  | | ||    || | ||||   ||      || |||||||||   || || || || | ||| ||||| ||||||||||| || ||||||||||||||||||||||||||||||||||| || |||||||| |  |
actgagctggtgaaacagattaaaatatgtgtatttcatctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttg-----ttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 1
------gaattttg-gttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
      ||  |  | ||    |  |   ||| ||  ||| |   |   |  || |  |     ||  | |||||  |   ||  | | |||  ||    | || |||||||||   || || |  || ||||| ||||| ||||||||||| || |||||||||||||||||||| ||||| |||||||| || ||||||||||| |
ttccttgagctaggagtaaagatacgtgcttcct--ttatttgtaagtagcttcatctcaaaatggctatctgtttaa--aacatgtattggattt---tattgcagTATCAACAAGATGACCCAGTTACCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTC

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 1
----------gaattttggttcttac-tctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
          || |   | |   ||  | ||  ||| | || | |      | ||   |     |  ||  | |||||  |   ||  | | |||| ||    | ||  ||||||||   || || |  || | ||| ||||| ||||||||||| || |||||||||||||||||||| ||||| |||||||| || |||||||||||  
cttgagctaggagtaaagatatatatgtttcctttattcgtaagt------agctcccagtcaacaatggctatctgtttaa--aacatgtattgcattt---tattgtagTATCAACAAGATGACCCAGTTATCCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACGTACAATTATTACAGCCTACCATTTTGCCGTT

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 1
gaattttggttcttactctctctt-----actagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
  |   ||| |||    |  | ||     |  | ||||      ||  | | || |     |  | || | | |||  |||  ||||||  |    ||  | ||||||||  | || |||||||| || || ||||||||||||||||| || || || |||||||||||||| |||||||| | ||| ||||||||||| | ||
agacactggctctgttacagtattcatgaaacacttaactgggaaatatgtgacttaaacataatattgtat-aaggaaatcatttttgttt----ctcctgcagTATCAGACAGATGAGCAGGTGACTCTGTGGGTAAACAAAGTTGGTCCTTACAATAATCCACAAGAAACCTACAACTACTTCAGCCTTCCATTTTGTCACC

upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 1
---gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
     | ||  || |||||| ||| | | ||| | |    | |  || || | ||| |      | |  |    | |   ||||||   ||   |||   ||||||||     | || | ||| ||||| |||||||| || ||||| || || || |||||||||||||| ||||| ||||| |||||||||||||| || |
atgctacttctgtacttactttctgtaagtagctcaaattacag-ctcttgcttttgttccagatgcactttgttaacagttttttaattttgtctt--gcagTATCAGCAGAATGAACCGGTTACCCTTTGGGTAAATAAGGTTGGACCTTACAATAATCCACAAGAAACGTACAATTATTATAGTCTTCCATTTTGTCGTC

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|125011347|gb|EL083616.1|EL083616
EST:     TCTCGTTTCCCTTCTCACTCCTACGTTCGCATCCGATTCAGATCACAAG                         TATCAAGCCGAGGA
genomic: TCTCGTTTCCCTTCTCACTCCTACGTTCGCATCCGATTCAGATCACAAGgtaagactcg ... cctttttcagTATCAAGCCGAGGA
EST: gi|125226410|gb|EL240495.1|EL240495
EST:     TTCTCGTTTCCCTTCTCACTCCTACGTTCGCATCCGATTCAGATCACAAG                         TATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTT
genomic: TTCTCGTTTCCCTTCTCACTCCTACGTTCGCATCCGATTCAGATCACAAGgtaagactcg ... cctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTT
EST: gi|125286179|gb|EL300264.1|EL300264
EST:     TTCTCGTTTCCCTTCTCACTCCTACGTTCGCATCCGATTCAGATCACAAG                         TATCAAGCCGAGGAGCAAGGTCACCCTATGAGTAAACAAAGTTGGCCCAT
genomic: TTCTCGTTTCCCTTCTCACTCCTACGTTCGCATCCGATTCAGATCACAAGgtaagactcg ... cctttttcagTATCAAGCCGAGGAGCA-GGTCACCCTATGGGTAAACAAAGTTGGCCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
                          tcaattttttttgcct  CT-rich tract
                       aagtcaatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattttggttcttactctctcttactagttaatcccataaacttttacatttctgtgcttttctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- attttgg
- - - - - - - - tctctct
- - - - - - - - - - - - - - - - - - cataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagtcaa