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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTACCCCATAGAGCGGCTGATCTACCTCCTAAGTTCAAATCAATGCTTGTTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgttttttttccttcaaattttcaacttttacatctctagtatgctttattttttttcgttaatgtcgttgtgggatcattctgtctgatgtaact...

Basic information

species Arabidopsis thaliana
transcript AT3G47810.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G47810.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G068489_T01 (Zea mays), 5'ss of exon 1
TGTACCCCATAGAGCGGCTGATCTACCTCCTAAGTTCAAATCAATGCTTGTTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgttttttttccttcaaattttcaacttttacatctctagtatgctttattttttttcgttaatgtcgttgtgggatcattctgtctgatgtaact-------
  | || ||  | ||| | || || ||  | || ||||| || ||||| || || || ||||| |||||||||||||||||||| |||||||||||||| |||   ||   || |   |          |       |  |  |  | | |      |     |||   || ||      || |   | || ||||  |        
CATCCCGCACCGGGCGCCCGACCTCCCCGCCAAATTCAAGTCCATGCTCGTGCCCGGCAAGATCCAACACATCATCTGCACTGGCAATCTCTGCATCAAGgtaaccttaccttccgcgcctggccg-gccggccgggtaaccggcgtccctcggcgatcgattttacaatcctt------tcctctcgcctcatgtgtccaattttt

upper sequence: AT3G47810.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G109315_T02 (Zea mays), 5'ss of exon 1
TGTACCCCATAGAGCGGCTGATCTACCTCCTAAGTTCAAATCAATGCTTGTTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgttttttttccttcaaattttcaacttttacatctctagtatgctttattttttttcgttaatgtcgttgtgggatcattctgtctgatgtaact-
  | || ||  | | | | || || ||  | || ||||| || ||||| || || || ||||| ||||||||||||||| |||| || ||||||||||| |||   |||   |||||        || | | |||||   ||  |||| |  ||||| || || |      ||  |       |   |   | || | |  
CATCCCGCACCGGGTGCCCGACCTGCCCGCCAAATTCAAGTCCATGCTCGTGCCCGGCAAGATCCAACACATCATCTGCGCTGGCAACCTCTGCATCAAGgtatcctttaccttcctctcttcgatcga-tcttacagtcctcatatgttcaattttgttgcgctggctaggtcctattgctgtgtggatagttgcatcac

upper sequence: AT3G47810.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA02G43610.3 (Glycine max), 5'ss of exon 3
TGTACCCCATAGAGCGGCTGATCTACCTCCTAAGTTCAAATCAATGCTTGTTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgttttttttccttcaaattttcaacttttacatctctagtatgctttattttttttcgttaatgtcgttgtgggatcattctgtctgatgtaact----
  ||||||| || ||| ||||||| ||| ||||||||||||| |||||||| ||||| ||||| || ||||| || || ||||||||| | || || |||||| |||     ||  || ||||  | |  | | |  ||  |  |     || |  |  | | ||    |  |  |  | |   |||   | ||     |    
CATACCCCACAGGGCGCCTGATCTTCCTGCTAAGTTCAAATCCATGCTTGTCCCTGGCAAGATCCAGCACATAATTTGTACTGGAAATTTATGTATTAAAgta-tgtccagctta-ttgaaataattatttctgat-tcagttttgactgttgtcatgctgcattggaat-ataatcagttgtctctactttatagttttcaac

upper sequence: AT3G47810.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA14G05340.2 (Glycine max), 5'ss of exon 2
TGTACCCCATAGAGCGGCTGATCTACCTCCTAAGTTCAAATCAATGCTTGTTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgttttttttccttcaaattttcaacttttacatctctagtatgctttattttttttcgt-taatgtcgttg--tgggatcattctgtctgatgtaact--
  ||||||| || ||  ||||||| ||| | ||||||||||| |||||||| || || ||||| |||||||| || || ||||||||| | || || |||||| |||     ||  || ||||  | |  | | |    ||   | ||  |  |    |  ||  ||||||  |    ||     | | | |    |  ||||  
CATACCCCACAGGGCACCTGATCTTCCTGCAAAGTTCAAATCCATGCTTGTCCCCGGCAAGATCCAACACATTATTTGTACTGGAAATTTGTGTATTAAAgta-tgtccagctta-ttgaaataattatttctgat---tcagttttgactgttgccatgccgcataatgtaatcaattgtctctactttatagttttcaactta

upper sequence: AT3G47810.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv17s0000g05880.t01 (Vitis vinifera), 5'ss of exon 1
TGTACCCCATAGAGCGGCTGATCTACCTCCTAAGTTCAAATCAATGCTTGTTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgt-agtgttttttttccttcaaattttcaacttttacatctctagtatgctttattttttttcgttaatgtcgttg----tgggatcattctgtctgatgtaact
| | ||  |||| ||  ||||| | || || ||||||||||| |||||||||||||| ||||| ||||||||||| |||||||| ||| | || |||||||| |||| ||||| | |||    |||||  |||| |    |||  |    |     || |||   || | |   ||    |||| | ||     |  |||||   
TATCCCTGATAGGGCTCCTGATTTGCCGCCAAAGTTCAAATCCATGCTTGTTCCTGGCAAGATCCAACACATCATTTGCACTGGGAATTTGTGTATCAAAgtcagtgctttttcttcttt--cttttcttctttcattcttctgttgctatgccagttatttaaatactatttctggacttgggtttatg--agcaaatgtagg-

upper sequence: AT3G47810.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S75_108V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTACCCCATAGAGCGGCTGATCTACCTCCTAAGTTCAAATCAATGCTTGTTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgttttttttccttcaaattt--tcaac--ttttacatctctagtatgctttattttttttcgt--taatgtcgttgtgggatcat-tct---gtctgatgtaact-----------------------------------------------------
  | ||  | ||||| || ||||| ||| |||||||||| || ||||| || || ||||||||||| |||||| || || |||| ||||| |||||||| ||  |       ||    ||  |    | |||   | | | | |  | | ||| | || | |||  ||  | || | |||  || || || |||   ||   |||                                                          
CATTCCATACAGAGCCGCGGATCTGCCTGCTAAGTTCAAGTCTATGCTAGTGCCCGGGAAGATTCAGCACATCCTCAGCCCTGGCAATCTTTGCATCAAGgttttcccgccctttacgcagctgcaataaacagctctccctgttgaatgtgcatcatatatttctgtgctcattttgtttgggaattatatctagggttcaatggggacatgctggggaggctcacgtcttagggtgctcattatggcaatcgcaattgcag

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|164085647|gb|ES150445.1|ES150445
EST:     TCCTGGGAAGATTCAACACATCATCTGCACTGGAAATACTCTGCATCAAA                         GAAATCCATGACTACT
genomic: TCCTGGGAAGATTCAACACATCATCTGCACTGGAAAT-CTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACT
EST: gi|116458131|gb|EG500723.1|EG500723
EST:     TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAA                         GAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
genomic: TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
EST: gi|19875481|gb|AU236312.1|AU236312
EST:     TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTNTGCATCAAA                         GAAATCCATGACTACTTGAANACTATCTGCCCTGATTCGCATATAGNTCGA
genomic: TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
EST: gi|116458125|gb|EG500717.1|EG500717
EST:     TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAA                         GAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
genomic: TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
EST: gi|164217961|gb|ES115277.1|ES115277
EST:     TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAA                         GAAATCCATGACTACTTGAAGACTATCTGCCCTGA
genomic: TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACTTGAAGACTATCTGCCCTGA
EST: gi|116458116|gb|EG500708.1|EG500708
EST:     TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAA                         GAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
genomic: TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
EST: gi|116458122|gb|EG500714.1|EG500714
EST:     TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAA                         GAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
genomic: TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
EST: gi|116458120|gb|EG500712.1|EG500712
EST:     TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAA                         GAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
genomic: TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
EST: gi|116458124|gb|EG500716.1|EG500716
EST:     TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAA                         GAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
genomic: TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
EST: gi|116458130|gb|EG500722.1|EG500722
EST:     TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAA                         GAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA
genomic: TTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgtttt ... actgttgtagGAAATCCATGACTACTTGAAGACTATCTGCCCTGATTTGCATATAGTTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTACCCCATAGAGCGGCTGATCTACCTCCTAAGTTCAAATCAATGCTTGTTCCTGGGAAGATTCAACACATCATCTGCACTGGAAATCTCTGCATCAAAgtagtgttttttttccttcaaattttcaacttttacatctctagtatgctttattttttttcgttaatgtcgttgtgggatcattctgtctgatgtaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttccttc