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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa...

Basic information

species Arabidopsis thaliana
transcript AT2G22230.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaa-atattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa
 |  |  || || |  || ||||||||||| || ||||| || ||||||||||| |||||||| |||||||| || |||||||||||||||||| ||||||||  | |   |  |    |   | |  |  |||  ||||   | | |  |||| | |    || | | |     | | |  || | ||  | ||   |  
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggcatccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctctcattgtggtc-

upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G055667_T01 (Zea mays), 5'ss of exon 3
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgta-ataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa
 |  |  ||||| || || |||||||| || || ||||| || |||||||| || ||||||||||||||||| || |||||||||||||||||| | |||||| |||||| ||   | |  || |    |||||    | | |      | |    || ||||| |   | |    |   ||       ||| || | |  
AGAATATGCTGTTGCAATCAAGAATGTGACAATAAATGATAACTTCTTCCCAGGGCATTTCCCTGAACGACCCATAATGCCTGGTGTTCTCATGGTCGAGgtatataatattctcgttatttttcctttttttgatacctacattgcttattgagatgcaattgtttcatcattattgacatgtagactaaagtgatgtt-

upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G024482_T01 (Zea mays), 5'ss of exon 2
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa---
 |  |  || || |  || |||||||| || || ||||| ||||||||||| || ||||| |||||||| || || ||||| ||||| |||||| | ||||||   |  |     |   |||||  |   |  |         ||||  |       |  ||||||| |||  |||  | | | |  | | | |   | |   
AGAATATGCAGTGGGGATCAAGAATGTTACAATAAATGATAATTTCTTCCCAGGACATTTTCCTGAACGCCCCATAATGCCCGGTGTCCTCATGGTCGAGgtatgcaccaattcattgtgttgctgatcatgtttagggtctggatcttactaacaatt-ttgatat-ttaattgtcct-tacatcaccagaggtgatgatcc

upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv12s0055g01100.t01 (Vitis vinifera), 5'ss of exon 3
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataa-taatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa
 ||||| ||||| || || |||||||| || || ||||| || ||||| ||||| ||||| || ||  | ||||| |||||||||||||||||| ||||||||||   |  |      |  ||  |||  ||| |  |     || |  | ||||||  || | | ||||  |  ||   ||   |       ||||  ||
AGTTTCTGCTGTTGCCATAAAGAATGTAACAATAAATGATAACTTCTTTCCTGGGCATTTTCCCGAGAGGCCAATTATGCCTGGTGTTCTCATGGTTGAGgtaatttcttgttcccgtaccttttaaatatttttttttctttagttgcattatttttaaagttacatgtatgaggtaa-atgtttccatttttgctacaa

upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EDP03190 (Chlamydomonas reinhardtii), 5'ss of exon 2
-----------------TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgt-aataataatcgtttaaagttgcaaacttttgtcctcaagaagat---caaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa
                     |  ||||| |     |||  ||||||||| || ||||| |||||||| ||||| ||||| || || || |||||||||||||      |  |||   | |  |   |    |    |         |  |  | |||  || |   || ||  |       ||  |   ||  ||   |                     
GTTGAGTGGGAGAAGGAGAAGTACGCTGTGGGCTACAAGTGTGTCACCATTAACGACAACTTCTTCCCAGGCCACTTCCCCGAGCGCCCTATCATGCCTGgtgagtgacttcttggcatcagcagcgactcgtctgggccatggcggtgcgcacgcaactagctgtacagatgctacagcgctgtcagcctacttgaatt---------------------

upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S137_144V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa-----
    || ||||| || ||||||||||| || |||||||||||||||||||| ||||| |||||  | || || |||||||| ||||| || ||| ||||||||| |     | |||  |  ||    ||  | | |    |    | |||     ||  | ||   | |  |    ||| |  |         ||||  |     
GCAGTCGGCTGTTGCCATTAAGAATGTGACTATCAATGACAATTTCTTCCCGGGCCACTTCCCCCAGCGGCCCATCATGCCCGGTGTGCTTATGGTTGAGgtaaga---cgcctttgcaaatgtttgctgattttcatgtgggtgtgaaacgcaatgccaatgggttat--gtcaatgtgtggcaacgttggcgcttctattgcc

upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S196_99V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaac-ttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa--
 |  || ||||| || || || ||||| || ||||||||||| ||||||||||| || |||||  | || || ||||||||||| || |||||| | |||||||  |      || |  | |   | | | |||   | ||    |      | |  | |     || || |  |  |||| |  | |    ||  | ||   
GGAGTCGGCTGTTGCCATAAAAAATGTGACTATCAATGACAACTTCTTCCCTGGTCACTTCCCCCAGCGGCCCATCATGCCTGGGGTGCTCATGGTAGAGgtaa-gacgtcatttcagggatttgatcatcttgatatgaatgtaacattgcagtgcgcatggtttaggtcaa-taatgtaatagtgtgggcat-ttctattt

upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaat-attttgtaattgatatgttagc--tgttgtattcctttcaaaatgctttaa----
 |  |||| ||| || |||||||| || || ||||||||||||||||||||||| || |||||  | ||||| |||||||||||||| |||||| ||||||| | |   | | |||     ||    ||  | ||     |||| | |||| |   || |||| |  | |  |   | |||   |    | | | |  | |      
GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagac--agcattt-----tgtgcgctaatctcaatgtgaaggtgaaattagactgcaatttacttctagggcatattgcgatagcatgacagttttattggttg

upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa
|||  | || ||||  ||||| || || || |||||||||||||||||||| ||||| || || ||  |||| ||||||||||| ||||||||| ||||||||  ||     |     ||    | | ||||   ||   | || || ||||  ||     |  ||  |   ||||                        
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatg-----agacagagaatttt---cttgcgtagttctaatacgttcatgcttttaaatcttctgtccag--------------------

upper sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ06529 (Selaginella moellendorffii), 5'ss of exon 3
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaata-ttttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa
|||  | || ||||  ||||| || || || |||||||||||||||||||| ||||| || || ||  |||| ||||||||||| ||||||||| ||||||||  ||     |     ||    | | ||||   ||   | || ||  ||  ||||| ||||  | |   ||                            
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgtagaaaacgatg-----agacagagaatttt---cttgcgtagttctcatgcttttgaaatttctgt-ccag----------------------------

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|164129844|gb|EL978509.1|EL978509
EST:     GACCAATCATGCCTGGTGTTCTCATGATTGAG                         GCAATGGCGCAAGTGGGAGGTATAGTAATGCTGCAGCCGGAAGTAGGAGGC
genomic: GACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataa ... tgtattgcagGCAATGGCGCAAGTCGGAGGTATAGTAATGCTGCAGCCGGAAGTAGGAGGC
EST: gi|163992823|gb|ES142806.1|ES142806
EST:     TGCCTGGTGTTCTCATGATTGAG                         GCAATGGCGCAAGTGGGAGGTATAGTAATGCTGCAGCCGGAAGTAGGAGGC
genomic: TGCCTGGTGTTCTCATGATTGAGgtaataataa ... tgtattgcagGCAATGGCGCAAGTCGGAGGTATAGTAATGCTGCAGCCGGAAGTAGGAGGC
EST: gi|86078864|gb|DR374621.1|DR374621
EST:     CTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAG                         GCAATGGCGCAAGTCGGAGGTATAGTAATGCTGCAGCCGGAAGTAGGAGGC
genomic: CTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataa ... tgtattgcagGCAATGGCGCAAGTCGGAGGTATAGTAATGCTGCAGCCGGAAGTAGGAGGC
EST: gi|164009888|gb|ES013630.1|ES013630
EST:     CTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAG                         GCAATGGCGCAAGTGGGAGGTATAGTAATG
genomic: CTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataa ... tgtattgcagGCAATGGCGCAAGTCGGAGGTATAGTAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaatattttgtaattgatatgttagctgttgtattcctttcaaaatgctttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagaaga