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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcacagagttcatccattcttttgctctgtgggttactaggatctatctaaatcctgttttgctaacccag

Basic information

species Oryza sativa
transcript LOC_Os03g04970.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 16
GTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcacagagttcatccattc--ttttgctctgtgggttactaggatctatctaaatcctgtt-ttgctaacccag--------------------------------
||||||||||||||||| ||||| || || || ||  ||||  || ||||||| || ||||||||| || || ||||||| || |||||||| || |||||||  |   |   |||   |  |||  | |||  ||      |   |  |  |||    ||    || || || |  | |                                
GTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTTGTTGGCAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAGCCAAAGgtaagggttctttgtttgccttttcactgttgtgcttacttctgtcaaaagatatagccatttcattgttactgattctgctgtcaattttttcttcctgctccgtgattag

upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 16
GTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcacaga-gttcatccattcttttgctctgtgggttactaggatctatctaaatcctg-ttttgctaacccag-------------------------------
|||| ||||||||| || ||||||||||| || ||  | ||  || ||||||| || ||||||||||| |||  ||||||||| |||||||| || |||||| | || |     |||      |||  | | | |||            ||     | || ||| || |||| ||                                   
GTGCTCACAATTGCATCAAATGCGGGTGTTGAGGGTGCAGTTGTTGTTGGCAAACTATTGGAACAGGAGAATCATGATCTAGGATATGATGCAGCCAAAGgt-gcgtgatttttgttttctttttccctagttgtgttttcattccatgtcagaagagatactgattctgctgacattttttgcaatttttttttctgcttcacaattag

upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 5'ss of exon 14
GTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgt-agtgtcacagagt-tcatccattc--ttttgctctgtgggttactaggatctatctaaatcctgttttgctaacccag
||  ||||||| ||||| ||||| || || |||||  |||| ||| |||||||||| ||||| || |||||  | || || ||||||||||||||||||||| ||| |||||     |||||  |||  ||||| ||| |  |    | | || || |||| |   |       || | ||
GTTTACACAATCGCTTCAAATGCTGGAGTTGAAGGTGCTGTTATTGTTGGCAAGCTCTTGGAGCAAGATAACCCAGACCTCGGTTATGATGCTGCTAAAGgtgagtttcacaatccatcatcacttcacttttgttctctctgaagattgcatttagctaactgtggag--aacaaactag

upper sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 15
GTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcacagagttcatccattcttttgctctgtgggttactaggatctatctaaatcc-tgttttgcta-acccag------------------------------------
||  |||| |||||||| ||||| || || || ||  | ||  |  | ||||||||||||||||| |||||| |||| || |||||||||||||||||||||            | |||    |  ||  || | |    | || | ||| | ||   |   | |||  ||| |  | |                                    
GTTTACACGATTGCTTCCAATGCTGGAGTCGAGGGTGCAGTTGTCGTAGGCAAGCTTTTGGAACAAGATAATCCTGACCTTGGTTATGATGCTGCTAAAGgttacactcttatatgcattagataattcactttctatagttcttg-atccaccttgttatatatttccctatattccgaaatctgaactagcttcttttggcatttactttcag

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|86536823|gb|CI177029.1|CI177029
EST:     CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTGGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|38481227|gb|CF965316.1|CF965316
EST:     CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAACGTCTGGTATCATTGACCCACTAAAAGTT
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAA-GTCTGGTATCATTGACCCACTAAAAGTT
EST: gi|88263413|gb|CI367187.1|CI367187
EST:     CAAGCTTTTGGAACA-GATAATACTGATCTAGGTTATGATGCTGGTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|89192064|gb|CI393421.1|CI393421
EST:     ATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: ATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88252372|gb|CI350800.1|CI350800
EST:     GAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: GAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88224758|gb|CI224607.1|CI224607
EST:     CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88446911|gb|CI528954.1|CI528954
EST:     TAGGTTATTATGCTGCTAAAG                         GTGAATACGTTNACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: TAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|86837997|gb|CI343294.1|CI343294
EST:     CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|86493378|gb|CI136011.1|CI136011
EST:     CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88518653|gb|CI446307.1|CI446307
EST:     TAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: TAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88455316|gb|CI519337.1|CI519337
EST:     ATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: ATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88506713|gb|CI434219.1|CI434219
EST:     TTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: TTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88487337|gb|CI424608.1|CI424608
EST:     GATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: GATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88481324|gb|CI418595.1|CI418595
EST:     CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88269636|gb|CI380934.1|CI380934
EST:     GTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: GTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88903313|gb|CI088851.1|CI088851
EST:     CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|86536911|gb|CI177117.1|CI177117
EST:     CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88483826|gb|CI421097.1|CI421097
EST:     GGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: GGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88842319|gb|CI081575.1|CI081575
EST:     CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: CAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
EST: gi|88845406|gb|CI084331.1|CI084331
EST:     AAGCTTTTGGAACAGGATAATACTGATCTAGGTTTATGATGCTGCTAAAG                         GTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA
genomic: AAGCTTTTGGAACAGGATAATACTGATCTAGG-TTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTA

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: 71 (upstream exon), 25 (downstream exon)
Score: 3

GTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcac ... gctaacccagGTGAATACGTTGACATGGTGAAGTCTGGTATCATTGACCCACTAAAAGTTATCAGAACAGCTCTGGTGGATGCTGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCACACAATTGCTTCGAATGCGGGTGTAGAAGGATCTGTCATTATTGGCAAGCTTTTGGAACAGGATAATACTGATCTAGGTTATGATGCTGCTAAAGgtagtgtcacagagttcatccattcttttgctctgtgggttactaggatctatctaaatcctgttttgctaacccag

- - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT