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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagtggcaatctttggagcagcaaatcattaagaggctaccctgaagaaaatgattggctggtcgtgtgaaattttcattttatctccttcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG

Basic information

species Oryza sativa
transcript LOC_Os05g46720.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G174990_T02 (Zea mays), 3'ss of exon 3
----agagtggcaatctttggagcagcaaatcattaagaggctaccct--gaagaaaatgattggctggtcgtgtgaaattttcattttatctccttcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG
    ||     || |       ||| ||  |  | ||| ||| ||  |  ||||||| || ||| ||   |  ||  | |     | | || | | |  |    |||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||| ||| | || ||||| |||||||| || |  ||||| ||||||
caatagccccacattaaaccttgca-catgtgctcaaggggccacgattagaagaaagtggttg-ctatcctagttgactgggattctcatttgcattgc----agGTTCCTAAAAGCACGGAAATTTGAAGTTGAGAAAGCTAAGAGTATGTGGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G355610_T01 (Zea mays), 3'ss of exon 3
--agagtggcaatctttggagcagcaaatcattaagaggctaccct--gaagaaaatgattggctggtcgtgtgaaattttcattttatctccttcacat-atagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG
          || ||||| |    ||  |  || |||||| |   |  ||||||| || | | |    |  ||  | |   |      |||| ||  |||   || ||||| ||||||||||||||||||||||||||||| |||| |||||||||||| |||||||||||||| |||||||| |||| |||||| ||||||
gccacacacaaaactttgta----catgtgcttgagaggccatgattggaagaaagtggtcg-ccatcctagttgactgggctgggattctcatttgcattgcagATTCCTAAAAGCACGGAAATTTGATGTTGAGAAAGCTAAGAATATGTGGTCAGACATGCTTAAATGGAGGAAGGAATTCGGGGTTGACAAAATAGAG

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 2
agagtggcaatctttggagcagca-aatcattaagaggctaccctgaagaaaatgattggctggtcgtgtgaaattttcattttatctccttcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAA---TATAGAG
 |||  |  ||||||| |    || | |    | |   ||| |    |  |  || ||| ||    || | | ||    |||  ||   ||     |  || ||| | |||||| ||||||||||| ||||||||||||||   |||||| |  | ||| |  | ||||| || |||| |||  |||| |    ||| |||
-gagatggtatctttgcatattcacagtttgcatgcttctaacacagatgacttgtttgccttaaagtataatataaaaattgaattaactgatgttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 3
agagtggcaatctttggagcagcaaatcatta--agaggctaccctgaagaaaatgattggctggtc-----gtgtgaaattttcattttatctccttcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG---
        | | | ||   || | | |  |||  | | | ||        |  ||| ||   |  |      || | | ||| | |       |   | || |  |||||| | |||||| |||| |||||| ||||||||||||||   |||||| | |||||| || | ||||| ||||| ||||| |||||||  ||   |   
-------tattttatgttccaactattttttattatatggtattgcttcaactatgttttcataatgagtaggtataacattgttaagagcattatattacttgcagGTTCTTGAAAGCAAGGAAGTTTGATATTGAGAAAGCAAAGCACATGTGGACTGATATGATTCAGTGGAGGAAGGATTTTGGTGCTGACACAATTTTGGAG

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|88417178|gb|CI576252.1|CI576252
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTC-TCAAAGCA
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCA
EST: gi|29628429|gb|CB633440.1|CB633440
EST:     GATGAGGACCTGTTGCCGCAACAGCATTATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|88299560|gb|CI574673.1|CI574673
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAG
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAG
EST: gi|29635388|gb|CB640397.1|CB640397
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCTTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29631056|gb|CB636065.1|CB636065
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29636608|gb|CB641617.1|CB641617
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29635051|gb|CB640060.1|CB640060
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29623352|gb|CB628363.1|CB628363
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29624625|gb|CB629636.1|CB629636
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|88401724|gb|CI591051.1|CI591051
EST:     GATGAGGACCTGTTGCCGCAACAGAATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACG
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACG
EST: gi|88386210|gb|CI572827.1|CI572827
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGG
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGG
EST: gi|29630847|gb|CB635856.1|CB635856
EST:     GATGAGGACCTGTTGCCGCAACAGCATTATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29628211|gb|CB633222.1|CB633222
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|33676711|gb|CF304950.1|CF304950
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|33676922|gb|CF305161.1|CF305161
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|25798393|gb|CA754354.1|CA754354
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGANATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|88399898|gb|CI585817.1|CI585817
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAG
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAG
EST: gi|88386060|gb|CI570695.1|CI570695
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|33657793|gb|CF280407.1|CF280407
EST:     ATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGGCTTAG                         GTTCCTCAAAGCACGGAAATTTTGATGTTGAGAAAGCAAAGAGTATTGTG
genomic: ATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATG-CTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTT-GATGTTGAGAAAGCAAAGAGTAT-GTG
EST: gi|29628534|gb|CB633545.1|CB633545
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|58595020|gb|CF993328.1|CF993328
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|88409627|gb|CI568917.1|CI568917
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTC-TCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|33675068|gb|CF303307.1|CF303307
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29669409|gb|CB665684.1|CB665684
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29665229|gb|CB661504.1|CB661504
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|88331717|gb|CI640748.1|CI640748
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29640888|gb|CB645895.1|CB645895
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
EST: gi|29636223|gb|CB641232.1|CB641232
EST:     GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAG                         GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC
genomic: GATGAGGACCTGTTGCCGCAACAGCATGATGATTATCACACAATGCTTAGgtacaagctt ... tcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaaatgattggctggtcgtgtgaaattttcattttatctccttcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG
                            ttttcattttatctcc  CT-rich tract
                       tgaaattttcatttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagtggcaatctttggagcagcaaatcattaagaggctaccctgaagaaaatgattggctggtcgtgtgaaattttcattttatctccttcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - -cagcaaa
- - - - - - - - - - - - - - - - - - - - ccctgaa
- - - - - - - - - - - - - - - - - - - - - - - -gaaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctgg