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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGCTGTTTCTTATGTGAAGTTCCTGTCCACCAATGAGCTTGCGTCTGCATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatgtgtcattgagatttttcttgcactgcaattatgaaattatgtttttgccttttaagcagctatgacttattagtaaaaagtgatgttttaggata...

Basic information

species Oryza sativa
transcript LOC_Os02g53140.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 13
GAAAGCTGTTTCTTATGTGAAGTTCCTGTCCACCAATGAGCTTGCGTCTGCATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatg-tgtcattgagatttttcttgcactgcaattatgaaattatgtttttgccttttaagcagctatgacttattagtaaaaagtgatgttttaggata---
|||||| || || ||||| || ||| | || | |||||||||||| ||||||||||| |||||||| ||||| |||||||||||||| || ||||  || ||||| | |   ||||||  | | | |     ||  || ||| |  |||||   ||||| || || | | |   | || | || |    |||| ||   ||   
GAAAGCAGTATCGTATGTCAAATTCTTATCTAACAATGAGCTTGCATCTGCATCAACAGATAGCACGTTACGTTTATGGGATGTCAAGGATAATTTGCCGgtatgctctttctgagatactccctccgtcctaa--attaaaattcgtttt-atctttttagtagat-tcatacaataattaatatatgtgttctatattatat

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G104920_T03 (Zea mays), 5'ss of exon 11
GAAAGCTGTTTCTTATGTGAAGTTCCTGTCCACCAATGAGCTTGCGTCTGCATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatg-tgtcattgagatttttcttgcactgcaattatgaaattatgtttttgccttttaagcagctatgacttattagtaaaaagtgatgttttaggata
|||||| || || |||||||| ||| | || | |||||||||||||||||||||||| |||||||||||||| |||||||||||||| || || ||||| ||||| | |   || |||  |   || | |  |  |||  |  ||| | | |   | |  |   || ||   |  |  | |     || ||     | |  
GAAAGCAGTATCATATGTGAAATTCTTATCTAACAATGAGCTTGCGTCTGCATCAACAGATAGCACATTACGCTTATGGGATGTCAAGGATAACTGCCCGgtatgctctttctgtgatagtgtgtgta-tatatatatatatatatatatatatatatatatatgccattcttcctctggagcttttgttgcaaaggaaag

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA14G05430.1 (Glycine max), 5'ss of exon 11
GAAAGCTGTTTCTTATGTGAAGTTCCTGTCCACCAATGAGCTTGCGTCTGCATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatgtgtcattgagatttttcttgcactgcaattatgaaattatgtttttgccttttaagcagctatgacttat-tagtaaaaagtgatgttttaggata-
||| |||||||| |||||||| || ||||| |   |||| ||||| ||||||||||| ||||| ||| | || ||||||||||| || ||||| |  || ||  ||   ||    |   |  || |  ||| |||      |||   | |  ||  |    | ||||  | | || |  | |  | | || || ||    | 
GAAGGCTGTTTCATATGTGAAATTTCTGTCTAATGATGAACTTGCTTCTGCATCAACAGATAGTACACTGCGATTATGGGATGTGAAGGAAAACTTACCAgtgagtaatatgagcaaaatgatttc-ttgctattgattggtta-actataaccaatctgcctgctagaagtcatgtgcttaccaataattttatactgaaa

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 5'ss of exon 11
GAAAGCTGTTTCTTATGTGAAGTTCCTGTCCACCAATGAGCTTGCGTCTGCATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatg--tgtcattgagatttttcttgcac-tgcaattatgaaattatgtttttgccttttaagcagctatgacttattagtaaaaagtgatgttttaggata
|||||| ||||| ||||| || ||  |||||| ||| ||||| || ||||| || || ||||||||| |||| ||||||||||||||||| || |  || ||  |  |              |||||||  | || | |  ||   |   || |      || |  | |     ||| |  | |                   
GAAAGCAGTTTCCTATGTTAAATTTTTGTCCAACAACGAGCTCGCTTCTGCGTCCACAGATAGCACACTACGCTTATGGGATGTCAAAGACAACTTGCCAgttagattactgcccgagccaatcttgcagattcagtcaaaaagaaaaacttgtcttgactatgttgttcaattttacttttcag------------------

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 5'ss of exon 11
GAAAGCTGTTTCTTATGTGAAGTTCCTGTCCACCAATGAGCTTGCGTCTGCATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatgtgtcattgagatttt-tcttgcactgcaattatgaaattatg--tttttgcctt-ttaagcagctatgactta--ttagtaaaaagtgatgttttaggata
|||||||||||| |||||||| ||| |||| | ||||||||| || ||||| || || || ||||||||  |||| |||||||| || |||||||  || ||| ||    |  |||| |  | ||    |    |  |  |||||||  ||||  ||   ||| ||    || |||||  ||    || | |||    |       
GAAAGCTGTTTCATATGTGAAATTCTTGTCAAACAATGAGCTCGCTTCTGCTTCTACAGACAGCACATTGAGGTTGTGGGATGTGAAGGAAAATTTGCCAgtaagtaaagtctagatatagttttttggtttcttcttacaattatggcttttaaccacattatgctttcataacttaggtttcctaagaatgagaagtc------

upper sequence: LOC_Os02g53140.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 5'ss of exon 11
GAAAGCTGTTTCTTATGTGAAGTTCCTGTCCACCAATGAGCTTGCGTCTGCATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgta------tgtgtcattgagatttttcttgcactgcaattatgaaatta-tgtttttgccttttaagcagctatgacttattagtaaaaagtgat-----gttttaggata---------------------------------------------------------------------
 ||||||||||| |||||||| ||| | || | |||||| ||||| || ||||| ||||| |||||||| || || ||||| || || ||||||   ||||||      | |||  ||    ||| | |||  ||           || | |   | ||  |  | |  | ||   | || ||     |   |||       |||| | | |                                                                     
AAAAGCTGTTTCGTATGTGAAATTCTTATCTAACAATGAACTTGCTTCCGCATCCACTGACAGCACATTGCGATTGTGGGACGTAAAGGAAAATATGCCTgtaagttattatgtttttattgtttattttgttctatccccgcattataaatccctctgtatggtga-tacctgccaatttttttagtacgttgaccatccatttttgcaaaatcttgtggaaattacatatggtacgaacaactaattcatctcaattcctttttcataatttttcttag

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|2310219|gb|C26374.1|C26374
EST:     ATCAACTGATAGCACATTACGGGTTATGGGATGTCAAAGNAAATTGCCCT                         GTAAGGGCATTCAGAGGGCAC
genomic: ATCAACTGATAGCACATTACGG-TTATGGGATGTCAAAGAAAATTGCCCTgtatgtgtca ... cctttttcagGTAAGGACATTCAGAGGGCAC
EST: gi|38476176|gb|CF960309.1|CF960309
EST:     ATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCT                         GTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCT
genomic: ATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatgtgtca ... cctttttcagGTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCT
EST: gi|29616392|gb|CB621404.1|CB621404
EST:     CATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCT                         GTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCT
genomic: CATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatgtgtca ... cctttttcagGTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCT
EST: gi|86492605|gb|CI135238.1|CI135238
EST:     ATTACGGTTATGGGATGTCAAAGAAAATTGCCCT                         GTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCT
genomic: ATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatgtgtca ... cctttttcagGTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 75 (downstream exon)
Score: 14

GAAAGCTGTTTCTTATGTGAAGTTCCTGTCCACCAATGAGCTTGCGTCTGCATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatgtgtca ... cctttttcagGTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGCTGTTTCTTATGTGAAGTTCCTGTCCACCAATGAGCTTGCGTCTGCATCAACTGATAGCACATTACGGTTATGGGATGTCAAAGAAAATTGCCCTgtatgtgtcattgagatttttcttgcactgcaattatgaaattatgtttttgccttttaagcagctatgacttattagtaaaaagtgatgttttaggata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtaaaaa