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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttctactttgttaacacttaacagagctttaggctcaagattagatgcaaaaagtatacaatgacgaagcatttcttgttcttttaaactgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTCCCATCTTCAAAGATGTATGATGCT

Basic information

species Arabidopsis thaliana
transcript AT4G32530.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G31060.1 (Glycine max), 3'ss of exon 2
----attttctactt-tgttaacacttaacagagctttaggctcaagattagatgcaaaaagtatacaatgacgaagcatttcttgttcttttaaactgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTCCCATCTTCAAAGATGTATGATGCT
    ||| ||||| | | |     | ||   ||  | |||   |||   || |  ||     |  |   |||| |     |||||| | ||||    | |  |||||| ||||| || |||||||||||||||||||| |||||||| || || || || ||||| || || || ||||| ||| | ||||| || ||||   | 
gtgaattatctacatatatcctggcataggtga--tatagttccaaatgtaaa--catttgttccatcttgacaacatgattcttgat-ttttgtggtatttcagTGTAATCTTCTGTGAAGCTGTTGCTATATATGGTGTTATTGTGGCTATTATTCTTCAAACCAAATTAGAAAGTGTTCCAGCATCAAATATTTATGCACCA

upper sequence: AT4G32530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0008g04760.t01 (Vitis vinifera), 3'ss of exon 2
-attttctactttgttaacacttaacagagctttaggctcaagattagatgcaaaaagtatacaatgacgaagcatttct----tgttcttttaaactgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTCCCATCTTCAAAGATGTATGATGCT
   | |  | |||   |   || | ||    ||  |  |   |||        |   ||      |||    ||| || |    || |   |||     |  |||||| ||||| || |||||||||||||||||||| || ||||| |||||||| || ||||||||||| |||||||| ||| | || || || ||||   ||
gtatatggatttttccagtgctaatca----ttcggagtttggat-gtcctttaggggtgcctcttgatattgcaattttgatctgatagcttatttcatttcagTGTAATCTTCTGTGAAGCTGTTGCTATATATGGTGTCATTGTGGCAATCATCCTACAAACAAAGTTAGAGAGTGTTCCAGCATCCAAAATATATGCACCT

upper sequence: AT4G32530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g05720.t01 (Vitis vinifera), 3'ss of exon 2
attttctactttgttaacacttaacagagctttaggctcaagattagatgcaaaaagtatacaatgacgaagcatttcttgttcttttaaactgtcc------cagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTCCCATCTTCAAAGATGTATGATGCT
     || | |    |||  |      |  |  || | |   |  | |||   |   |     ||      |  |   ||  ||||||    ||| |       ||||||||||| || || |||||||||||||||||||||||||| |||||||| || ||||||||| | |||||||| ||  | || || || ||||   | 
-----ctgcatgcacaacgatactgcaaattgcagaccccttaagaaatgatgattttgacttatttttttg-gtccttttctcttttggggtgttcggttcttagTGTCATCTTCTGTGAGGCTGTTGCTATATATGGAGTTATTGTGGCAATCATTCTTCAAACAAAGCTAGAGAGTGTGCCTGCATCCAATATTTATGCACCG

upper sequence: AT4G32530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S96_87V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------attttctactttgttaacacttaacagagctttaggctcaagattagatgcaaaaagtatacaatgacgaagcatttcttgttcttttaaactgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTCCCATCTTCAAAGATGTATGATGCT
                                                                           ||   | |  |   |  |||  |    ||| || |  | |||||   |||   | ||       |    || |  |||  ||| |  | | | | ||||| || || |||||||| || ||||| || ||||| ||||| || ||||||||||| || |||||||||  ||         |         |||| | 
gtgatttgtgaaacttgtagtattctacattttcttttttaaacctctcccccgctcccttcctctcttcctccctttcccctcatgctctgttatgaagattttgggttttaaattag---caagtggcattt-----ctggccactgattggccttatgtattctgc-agTGTGATTTTCTGCGAAGCAGTGGCTATCTACGGAGTGATTGTAGCTATCATACTGCAGACTAAGTTGGAGGCTGCTAAGCAGCCGTTTCACCCTGATTCC

upper sequence: AT4G32530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S35_224V6.2 (Physcomitrella patens), 3'ss of exon 2
--------------------------attttctactttgttaacacttaacagagctttaggctcaaga--ttagatgcaaaa--agt--atacaatgacgaagcatttcttgttcttttaaactgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTCCCATCTTCAAAGATGTATGATGCT
                            | ||| || ||      |||  |    | | |     ||||  || | |||  ||  ||    |  |||  |     | |  | |  |||    | | |  |||||| || ||||||||||| ||||| || ||||| |||||||| || ||||||||||| || ||||||||||    |       |         |||| | 
gtgaagtggacatcttgaagtgtcgcggtctctcctctgccccttctttccctcccctgacatggaagaaattgggtgctgaatcagctggtggaatctctggctactgatcgagcttacggatt-ttgcagTGTGATTTTTTGCGAAGCAGTTGCCATCTATGGTGTTATTGTAGCGATCATACTGCAGACCAAGTTGGAGACAACCAAGGAACCGTTTCACCCTGATTCC

upper sequence: AT4G32530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S143_106V6.1 (Physcomitrella patens), 3'ss of exon 2
------------attttc---tactttgttaacacttaacagagctttaggctcaagattagatgcaaaaagtatacaatgacgaagcatttcttgttcttttaaactgtcc-cagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTCCCATCTTCAAAGATGTATGATGCT
            || ||    || |   || |   ||  |     |||       |  || || |   |||   |    ||       |||        | | ||| | |   |||||| || || |||||||| || ||||| |||||||| ||||| || |||||||||||||| ||||||||         |    |          ||| | 
gtgagctgagagatattgaagtattggatttattttttccccctgtttgtagctgattttggacgttgaaatggt--tgtgttttgttattgagcagcttgtgaaattctatgcagTGTAATTTTCTGCGAAGCGGTGGCTATCTATGGAGTGATTGTAGCCATCATACTGCAAACCAAGTTGGAAGCCACAAAACAACCTTTTCACCCCGATTCC

upper sequence: AT4G32530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ29603 (Selaginella moellendorffii), 3'ss of exon 2
attttctactttgttaacacttaacagagctttaggctcaagattagatgcaaaaagtatacaatgacgaagcatttcttgttcttttaaactgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTC--CCATCTTCAAAGATGTATGATGCT
      || ||  ||    |||  | | |||    |||     || | |     ||  |   ||| |||                   | | |||   ||||| || |||||||| |||||||| || ||||||||||| ||||| |||||  |||| || ||| |||||  ||||   |      |       |    |  
-----gtatttctttttttcttt-ctgcgctccttgcttgttctttggttgctcaaagagctaatcacg------------------cataatgttttagTGTGATTTTTTGCGAGGCTGTTGCAATCTATGGAGTTATAGTTGCCATCATCTTGCAGACTAAGCTGGAGTCTGTCACTCGAGACTACCAGCACACAGCG--

upper sequence: AT4G32530.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ12101 (Selaginella moellendorffii), 3'ss of exon 2
attttctactttgttaacacttaacagagctttaggctcaagattagatgcaaaaagtatacaatgacgaagcatttcttgttcttttaaactgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTC--CCATCTTCAAAGATGTATGATGCT
      || ||  ||     ||  | | |||    |||     || | |     ||  |   ||| |||                   | | |||   ||||| || |||||||| |||||||| || ||||||||||| ||||| |||||  |||| || ||| |||||  ||||   |      |       |    |  
-----gtatttcttttttcttt--ctgcgctccttgcttgttctttggttgctcaaagagctaatcacg------------------cataatgttttagTGTGATTTTTTGCGAGGCTGTTGCAATCTATGGAGTTATAGTTGCCATCATCTTGCAGACTAAGCTGGAGTCTGTCACTCGAGACTACCAGCACACAGCG--

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|124893032|gb|EH971934.1|EH971934
EST:     GTATTACTTCGAAGAATCTCATCAG                         TGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAAT
genomic: GTATTACTTCGAAGAATCTCATCAGgttcgttaaa ... actgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAAT
EST: gi|116443834|gb|EG486426.1|EG486426
EST:     ATCGGTGCGGCTATAGAAGCTCCTCGTATTACTTCGAAGAATCTCATCAG                         TGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCAT
genomic: ATCGGTGCGGCTATAGAAGCTCCTCGTATTACTTCGAAGAATCTCATCAGgttcgttaaa ... actgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCAT
EST: gi|124709944|gb|EH801346.1|EH801346
EST:     ATCGGTGCGGCTATAGAAGCTCCTCGTATTACTTCGAAGAATCTCATCAG                         TGTCATCTTTTGCGAAGCTGTT
genomic: ATCGGTGCGGCTATAGAAGCTCCTCGTATTACTTCGAAGAATCTCATCAGgttcgttaaa ... actgtcccagTGTCATCTTTTGCGAAGCTGTT
EST: gi|164097310|gb|EL999034.1|EL999034
EST:     ATCGGTGCGGCTATAGAAGCTCCTCGTATTACTTCGAAGAATCTCATCAG                         TGTCANCTTTTGCGAAGCTGTTGCTATATATGGAGTT
genomic: ATCGGTGCGGCTATAGAAGCTCCTCGTATTACTTCGAAGAATCTCATCAGgttcgttaaa ... actgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTT
EST: gi|164139542|gb|EL990422.1|EL990422
EST:     ATCGGTGCGGCTATAGAAGCTCCTCGTATTACTTCGAAGAATCTCATCAG                         TGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTA
genomic: ATCGGTGCGGCTATAGAAGCTCCTCGTATTACTTCGAAGAATCTCATCAGgttcgttaaa ... actgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgcaaaaagtatacaatgacgaagcatttcttgttcttttaaactgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTCCCATCTTCAAAGATGTATGATGCT
                                              ctgtccc  CT-rich tract
      aaaaagtatacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttctactttgttaacacttaacagagctttaggctcaagattagatgcaaaaagtatacaatgacgaagcatttcttgttcttttaaactgtcccagTGTCATCTTTTGCGAAGCTGTTGCTATATATGGAGTTATTGTTGCAATCATACTGCAAACAAAGTTGGAGAGTGTCCCATCTTCAAAGATGTATGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG