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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggttgcgttgaagaaacatatctaatataaatatgccattctatcatgacacttgtttatcctttctctcag

Basic information

species Oryza sativa
transcript LOC_Os05g46720.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46720.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G355610_T01 (Zea mays), 5'ss of exon 4
GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggttgcgttgaagaaacatatc-taatat---aaatatgccattctatcatgac---acttgtttatcctttctctcag----------------
 ||||| ||||||||||||||||||||||||||||| |||| |||||||||||| |||||||||||||| |||||||| |||| |||||| ||||||||||| | |   ||| ||  | |||| | ||||||   | |  |  || ||| ||        || | | |||  |  | ||                   
ATTCCTAAAAGCACGGAAATTTGATGTTGAGAAAGCTAAGAATATGTGGTCAGACATGCTTAAATGGAGGAAGGAATTCGGGGTTGACAAAATAGAGgtaaa-gctgaagttaaattagcataccataatatttcatagttatcaatctttctcagagtaacctctatattttaacccttcttggttctataactcag

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G174990_T02 (Zea mays), 5'ss of exon 4
GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggttgcgttgaagaaacatatctaatataaatatgccatt-ctatcatgacacttgtttatcctttctctcag------------------------
|||||| ||||||||||||||||| ||||||||||| ||||||||||||||||| ||| | || ||||| |||||||| || |  ||||| ||||||||||||   ||   | ||  | ||||||  | ||||       ||  | |   |  | |    | |    |    || |                        
GTTCCTAAAAGCACGGAAATTTGAAGTTGAGAAAGCTAAGAGTATGTGGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaa--ctgaagttaaatagcatatcataaataatgccataatcgccaatgttgctcagagtaacttctgtgttctgacccttcttggtcctatacttcag

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA14G07850.1 (Glycine max), 5'ss of exon 3
GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAA---TATAGAGgtaaaaggttgcgttgaagaaacatatctaatataaatatgcc-attctatcatgac-acttgtttatcctttctctcag-------------------------------------------------
 ||| | |||||| ||||||||||| ||||||||||||||   |||||| |  | ||| |  | ||||| || |||| |||  |||| |    ||| ||||| |    |    ||  | ||| |||   ||  ||  |  |   || || |  |      |    | | || | | |  |                                                 
ATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAGgtgagttatccgatttgaaaaatataatcaacttattttggttgatcctgttttatttgatcaactgtactgtttttttgaaatcgttgttcatgctatactactttggtttcctgtctttctctttag

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 4
GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggttgcgttgaagaaacatatctaatataaatatgccattctatcatgacacttgtttatcctttctctcag----------------------------
|||| | |||||| |||| |||||| ||||||||||||||   |||||| | |||||| || | ||||| ||||| ||||| |||||||  ||   ||  |    | |   |      |  |  || |  |   |     ||| | |||  | |||| |     ||  || | ||                            
GTTCTTGAAAGCAAGGAAGTTTGATATTGAGAAAGCAAAGCACATGTGGACTGATATGATTCAGTGGAGGAAGGATTTTGGTGCTGACACAATTTTGG--AGgtatcgatatctgatgatttgcctgaatttggtgatggattat-tcaaaatacttttggcatctggctttgagttaatatattttctatgcttttgtaaag

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|29628429|gb|CB633440.1|CB633440
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29635388|gb|CB640397.1|CB640397
EST:     GGTCAGATCTGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTA
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTA
EST: gi|29631056|gb|CB636065.1|CB636065
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29636608|gb|CB641617.1|CB641617
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29635051|gb|CB640060.1|CB640060
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29623352|gb|CB628363.1|CB628363
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29624625|gb|CB629636.1|CB629636
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29630847|gb|CB635856.1|CB635856
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29628211|gb|CB633222.1|CB633222
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|33676711|gb|CF304950.1|CF304950
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|33676922|gb|CF305161.1|CF305161
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|25798393|gb|CA754354.1|CA754354
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGANATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29628534|gb|CB633545.1|CB633545
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|33675068|gb|CF303307.1|CF303307
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACT-CACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29669409|gb|CB665684.1|CB665684
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29665229|gb|CB661504.1|CB661504
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29640888|gb|CB645895.1|CB645895
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
EST: gi|29636223|gb|CB641232.1|CB641232
EST:     GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAG                         GAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT
genomic: GGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggtt ... tttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAATATAGAGgtaaaaggttgcgttgaagaaacatatctaatataaatatgccattctatcatgacacttgtttatcctttctctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA