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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaagatctttgctttaaatcacattttcttcatggatttgtttacatttggcttattgagtgtagagtgtgaacaatctgctatgaagttcgtaaaatt...

Basic information

species Arabidopsis thaliana
transcript AT5G10360.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10360.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 5'ss of exon 2
TTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaagatctttgctttaaatcacattttcttcatggatttgtttacatttggcttattgagtgtagagtgtgaacaatctgctatgaagttcgtaaaatt---
|||||| ||||||| |||||||||||||| || ||||| ||||||||||||||||| || || |||| ||  ||   | ||   || |  | |       ||| ||||   |  ||  |       | | |  |      |||||    ||   | ||     |    
TTCAACATCGCCAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtgctcctccttctctctctctcttgatgctgatctgttctgaaatgcgtggagatctcttgcatcgtgttaatctagcttg---tccgctcggtcctt

upper sequence: AT5G10360.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 5'ss of exon 2
TTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaag-atctttgctttaaatcacattttcttcatggatttgtttacatttggcttattgagtgtagagtgtgaacaatctgctatgaagttcgtaaaatt----
|||||| |||| || |||||||||||||| || ||||| ||||||||||||||||| || || |||| || ||  | ||      || |   ||  |  | | ||     | ||| |    | || |||| |   |||  ||| | |  |   ||  || |   ||    
TTCAACATCGCGAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtattctcgccgccgctcccccgtttgtt-tcgtttccccaatattagagagagtg-gtgttggtagtgg-caagccg--aatcagcgcgaacccttgtgt

upper sequence: AT5G10360.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G45770.1 (Glycine max), 5'ss of exon 2
TTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaagatctttgctttaaatcacattttcttcatggatttgtttacatttg-gcttattgagtgtagagtgtgaacaatctgctat-gaagttcgtaaaatt---
|||||| |||| ||||| ||||| || || || ||||| ||||||||||| |||||||  |||||||||     ||  || |       ||||  | ||  | |  ||   ||||   ||| ||    || | ||  |     | |||| |  |||   ||  | ||   
TTCAACATCGCGAATCCCACCACTGGATGCCAGAAGAAGCTCGAGATCGACGACGATCTGAAACTgtaa-----ttatttcactcttttttttaattataaaatatttcgtatttctacttgttcttggtggtgttcgtgtgttgtgctttcaaagaaagttgatttatt

upper sequence: AT5G10360.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 1
TTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaagatctttgctttaaatcacattttcttcatggatttgtttacatttggcttattgagtgtagagtgtgaacaatctgctatgaagttcgtaaaatt
|||||| |||| | ||| ||||| || || || ||||| ||||||||||| |||||||| |||||||||   |||  || |   |  | || | ||  |||  ||   |   |  |  ||  |   |||     |||       ||   ||   || |  | |  
TTCAACATCGCGAGTCCCACCACTGGATGCCAGAAGAAGCTCGAGATCGACGACGATCAGAAACTgtaatcacttcactctttctttctttctttttttggtgttaaatttttgagtatttctacttgttcttcgtggtgttcgtgtgttgtgctttgagagaaa

upper sequence: AT5G10360.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 5'ss of exon 2
TTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaagatctttgctttaaatcacattttcttcatggatttgtttacatttggcttattgagtgtagagtgtgaacaatctgctatgaagttcgtaaaatt-------
|||||  |||| ||||| || || || ||||| ||||| |||||||| ||||||||||| |||||||||| | |    ||     ||| |||| ||      ||  | | | ||| | ||  ||||   |   |   ||  ||  | ||      |  ||   ||       
TTCAATATCGCAAATCCTACTACAGGATGTCAGAAGAAGCTCGAGATTGATGACGATCAGAAACTgtaagctttcaaattc---ccacgtttttttttc---ttcctatgcgttttg-ttgctgagaaaatgatagaaattattagttaatgttgttttaggttttttttcc

upper sequence: AT5G10360.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S311_33V6.2 (Physcomitrella patens), 5'ss of exon 2
TTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaag-atctttgctttaaatcacattttcttcatggatttgtttacatttggcttattgagtgtagagtgtgaacaatctgctatgaagttcgtaaaatt---------------------------------------------------------------------------------------------------------
 | ||  |||| || || || || |||||||| |||||| |||||||||||||||||   || |||| || ||  ||||  | |      |||| |||  |||||| | ||   | |  ||  | |||    ||||    ||  | | |  |||  | ||    ||                                                                                                         
CTAAATATCGCTAACCCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattgttgcgctga------ttttattcgaggatttctgtattctcgatttgattagttgttagtgccctcatgcggattcgaatcttgttttcttagatctctatggcgctacctttcaatgttataaatgtagggaggtaaagttattagggtttagtgaggagactttgagtctaatatcctgcacttgcaattgtag

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|124789122|gb|EH878801.1|EH878801
EST:     ATCGATGACGATCAAAAACT                         CCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
genomic: ATCGATGACGATCAAAAACTgtaagatctt ... tttgatgcagCCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
EST: gi|116469836|gb|EG512428.1|EG512428
EST:     CCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACT                         CCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
genomic: CCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaagatctt ... tttgatgcagCCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
EST: gi|116420455|gb|EG463047.1|EG463047
EST:     CCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACT                         CCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGT
genomic: CCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaagatctt ... tttgatgcagCCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGT
EST: gi|125219080|gb|EL233165.1|EL233165
EST:     CGATCAAAAACT                         CCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
genomic: CGATCAAAAACTgtaagatctt ... tttgatgcagCCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
EST: gi|116469839|gb|EG512431.1|EG512431
EST:     CCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACT                         CCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
genomic: CCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaagatctt ... tttgatgcagCCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
EST: gi|124731981|gb|EH823383.1|EH823383
EST:     TGACGATCAAAAACT                         CCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
genomic: TGACGATCAAAAACTgtaagatctt ... tttgatgcagCCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
EST: gi|164107881|gb|ES007223.1|ES007223
EST:     GATCGATGACGATCAAAAACT                         CCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT
genomic: GATCGATGACGATCAAAAACTgtaagatctt ... tttgatgcagCCGCGCCTTTTTCGACAAGAGGCTCTCTCAGGAAGTTAGCGGAGATGCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAACGTCGCCAATCCGACCACCGGGTGTCAAAAGAAACTCGAGATCGATGACGATCAAAAACTgtaagatctttgctttaaatcacattttcttcatggatttgtttacatttggcttattgagtgtagagtgtgaacaatctgctatgaagttcgtaaaatt

- - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaacaa