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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGAGTAAATTGATCGATCTTCTAAACGGATCAGATTATGTTCCAACATATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagtatttttatatctttaaatttatatatgaattattattataaatacgtctatacaaaatatttatttacatgttgtttggactattttag

Basic information

species Arabidopsis thaliana
transcript AT3G04730.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04730.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g53150.1 (Oryza sativa), 5'ss of exon 3
ATGAGAGTAAATTGATCGATCTTCTAAACGGATCAGATTATGTTCCAACATATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagt-atttttatatctttaaatttatatatgaattattattataaatacgtctata--caaaata---tttatttacatgttgtttggactatt----ttag-------------------
    ||  ||  |||  ||  |    || || || |||  |||| |||| |||||||| || ||||| |||||||||||||| ||||| || |||||| |||  || | |  |  ||  ||         ||    || |  ||||          ||    | |||    ||||   | |    |||     |  |    ||||                   
---GGAACAATATGAATGAGGT---GAATGGCTCTGATGCTGTTACAACTTATGAAGACAAGGATGGTGACTGGATGCTTGTTGGAGATGTCCCGTGGCAgtatgttactacttcattcttgtgcccccttaactgttttccttattttccacctcatgattagaatgcggtttagcgataccacgttcaagtttctcgcattagctgattggttactctgcag

upper sequence: AT3G04730.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G159285_T01 (Zea mays), 5'ss of exon 3
ATGAGAGTAAATTGATCGATCTTCTAAACGGATCAGATTATGTTCCAACATATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagtatttttatatctttaaatttatatatgaattattattataaatacgtctatacaaaatatttatttacatgttgtttggactattttag---------
||||| | ||| |  | ||||   | | |||  | |||   ||  | || || ||||| || ||||||||||||||||| || || ||||| ||||||||||  || | |  ||     |        || |    | | || |   | | ||  |  |   |  ||   ||| ||| ||  | |   ||| | |         
ATGAGGGAAAACTAGTTGATCCGGTCAGCGGTGCTGATGTGGTCACTACTTACGAAGACAAGGATGGCGACTGGATGCTCGTTGGCGACGTCCCGTGGGAgtatgt-tctgcattctagtgtgccatcatctaggatttgatcaggcaaatgttcaggcttcagcttc--ttatatgctgccttgttgattgttgtccctgcag

upper sequence: AT3G04730.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G40760.1 (Glycine max), 5'ss of exon 2
ATGAGAGTAAATTGATCGATCTTCTAAACGGATCAGATTATGTTCCAACATATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagt----atttttatatctttaaatttatat---atgaattattattataaatacgtctatacaaaatatttatttacatgttgtttggactattttag
| ||||| |||||||| |||||||| ||||| || ||||| || ||||| |||||||| |||||||  ||||||||||| || || |||||||||||||||| |||    |   |||| ||| |||    | |    ||   | |||||||  |  |  |||  |  ||| ||| | | |  ||   | |  | | |   ||
ACGAGAGCAAATTGATTGATCTTCTCAACGGCTCTGATTACGTACCAACCTATGAAGACAAAGATGCTGACTGGATGCTCGTTGGTGACGTACCGTGGGAgtaagtctggaccattatttctctaagcacacaccacatccttaattattaggaccatttctcgattaaacatt-actaatttgg-atatataatttcacag

upper sequence: AT3G04730.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv14s0081g00010.t01 (Vitis vinifera), 5'ss of exon 3
ATGAGAGTAAATTGATCGATCTTCTAAACGGATCAGATTATGTTCCAACATATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagt----attttt----atatctttaaattta---tatatgaattattattataaatacgtctatacaaaatatttatttacatgttgtttggact-attttag
||||||| ||||||||||||||| | ||||| || ||||| || || || |||||||| |||||||| |||||||||||||| |||||||| || ||||||| |||    |  |||    |||| ||  ||||||   | | | ||    |   || |||   || ||| |   || | ||| |    |  || | | |    | ||
ATGAGAGCAAATTGATCGATCTTTTGAACGGTTCCGATTACGTGCCTACTTATGAAGACAAAGATGGAGACTGGATGCTTGTTGGAGACGTGCCATGGGAgtaagttacaacatttgacaatattttccaatttaaattgtttcaaaggcttacatcaattaatccatagattttactaattaatccttctttggaatttgaatcag

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|125060546|gb|EL129223.1|EL129223
EST:     TATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGA                         GATGTTTGTTGATT
genomic: TATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagtattt ... actattttagGATGTTTGTTGATT
EST: gi|116458903|gb|EG501495.1|EG501495
EST:     TATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGA                         GATGTTTGTTGATTCATGCAAACGTATACGAATAATGAAGGGATCAGAAGC
genomic: TATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagtattt ... actattttagGATGTTTGTTGATTCATGCAAACGTATACGAATAATGAAGGGATCAGAAGC
EST: gi|124858507|gb|EH942944.1|EH942944
EST:     TATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGA                         GATGTTTGTTGATTCATGCAAACGTA
genomic: TATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagtattt ... actattttagGATGTTTGTTGATTCATGCAAACGTA
EST: gi|47829393|gb|CK119077.1|CK119077
EST:     TATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGA                         GATGTTTGTTGATTCATGCAAACGTATACGAATAATGAAGGGATCAGAAGC
genomic: TATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagtattt ... actattttagGATGTTTGTTGATTCATGCAAACGTATACGAATAATGAAGGGATCAGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAGAGTAAATTGATCGATCTTCTAAACGGATCAGATTATGTTCCAACATATGAAGATAAAGATGGCGACTGGATGCTTGTAGGAGACGTACCGTGGGAgtgagtatttttatatctttaaatttatatatgaattattattataaatacgtctatacaaaatatttatttacatgttgtttggactattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA