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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCGTAGTGCAGTGCAAAATGTTGCCAAGTATTTCCCTACCGCGATCATTAGTGGAAGAAGCCGGGATAAGgtaatctttctacatgttttattttcttcatcaagaacattttcttgtgtgatctaatgtaataatagtacattttgcttcatctag

Basic information

species Arabidopsis thaliana
transcript AT5G51460.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G51460.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G47630.1 (Glycine max), 5'ss of exon 4
ATGCGTAGTGCAGTGCAAAATGTTGCCAAGTATTTCCCTACCGCGATCATTAGTGGAAGAAGCCGGGATAAGgtaatc------tttctacatgttttattttcttcatcaagaacattttcttgtgtgatctaatgtaataatagtacattttg--cttca-tctag-----------------------------------------
||||||  ||| ||  |||| || ||  | ||||| || |||||||| ||||||||||||||||| || |||||| |       |||    |      |   | ||| |       |||||         |   |  ||| ||   | | | |||  ||||| | | |                                         
ATGCGTGCTGCTGTTAAAAAAGTGGCGGAATATTTTCCAACCGCGATAATTAGTGGAAGAAGCCGTGACAAGgtatttaaagaattttataaaacaaaacaattttctttctcggtatttttactcacacttgcacataacaaatttccttgttgatcttcagttttgacttttgattttaacctttgttacataccctattggctcag

upper sequence: AT5G51460.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G13880.1 (Glycine max), 5'ss of exon 4
ATGCGTAGTGCAGTGCAAAATGTTGCCAAGTATTTCCCTACCGCGATCATTAGTGGAAGAAGCCGGGATAAGgtaatc-------tttctacatgttttattttcttcatcaaga-acattttcttgtgtg-atctaatg--------taataatagtacattttg-cttca--tctag---------------------------
||||||  ||| ||  |||  || ||  | ||||| || |||||||| ||||||||||||||||| || |||||| |        ||| || |      ||||||||  ||  |  |  ||| ||    || |  |||          |  | ||  |   ||||| ||| |  | ||                            
ATGCGTGCTGCTGTTAAAATAGTGGCGGAATATTTTCCAACCGCGATAATTAGTGGAAGAAGCCGTGACAAGgtacttggagaattttataaaacaaccattttctttctcttggtatttttactcacctgtacataacaagtttctttgttgatcatcggttttgactttaattttaacctttgttacatacgctattggatcag

upper sequence: AT5G51460.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 5'ss of exon 3
ATGCGTAGTGCAGTGCAAAATGTTGCCAAGTATTTCCCTACCGCGATCATTAGTGGAAGAAGCCGGGATAAGgtaatc--------tttctacatgttttattttctt-----catcaagaacattttctt--gtgtgatctaatgtaataatagtacattttgcttcatctag---------------------------------
||||||  | | |||  ||| || || |||| |||||| ||||| || |||||||||||||| ||||||||||||||         |||     |||  |||| | ||     ||| | |   |||| ||    | |     | | |        || ||  |  |||||||                                   
ATGCGTGCTACTGTGAGAAACGTGGCTAAGTTTTTCCCAACCGCAATAATTAGTGGAAGAAGTCGGGATAAGgtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccatttatatcagttttccttctatagatggtttttcatcttcactgacttgttacgtaacctactattcatttag

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|125236967|gb|EL251052.1|EL251052
EST:     TTGCCAAGTATTTCCCTACCGCGATCATTAGTGGAAGAAGCCGGGATAAG                         GTGTATGAGTTTGTTAATTTGAGTGAACTTTATTACGCCGGAAGCCATGGA
genomic: TTGCCAAGTATTTCCCTACCGCGATCATTAGTGGAAGAAGCCGGGATAAGgtaatctttc ... cttcatctagGTGTATGAGTTTGTTAATTTGAGTGAACTTTATTACGCCGGAAGCCATGGA
EST: gi|125299235|gb|EL313320.1|EL313320
EST:     TTGCCAAGTATTTCCCTACCGCGATCATTAGTGGAAGAAGCCGGGATAAG                         GTGTATGAGTTTGTTAA
genomic: TTGCCAAGTATTTCCCTACCGCGATCATTAGTGGAAGAAGCCGGGATAAGgtaatctttc ... cttcatctagGTGTATGAGTTTGTTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCGTAGTGCAGTGCAAAATGTTGCCAAGTATTTCCCTACCGCGATCATTAGTGGAAGAAGCCGGGATAAGgtaatctttctacatgttttattttcttcatcaagaacattttcttgtgtgatctaatgtaataatagtacattttgcttcatctag

- - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC