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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTGTTGAATATGCCGAGGGAGACTGTGTCCGTATTCTTCCATGCAATCATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatggattaatctaaataatttataatttgcataagtaaatgaacagaactgcggtcaacatgctattgttacctctttatgtcagagctctatag...

Basic information

species Oryza sativa
transcript LOC_Os05g32350.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g32350.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G135909_T01 (Zea mays), 5'ss of exon 5
GCCTTGTTGAATATGCCGAGGGAGACTGTGTCCGTATTCTTCCATGCAATCATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatg-atggattaatctaaataatttataatttgcataagtaaatgaacagaactgcggtcaacatgctattgttacctctttatgtcagagctctatag-----
|||||||||||||||  |||||||| ||  ||||||| ||||||||| |||||||||| ||||||||||| ||||| |||||| | || ||||| |||||||||  ||    | || |||  |||    | | |  ||  ||   |||||||   || ||      |  |||    | ||    |    | |   ||  |      
GCCTTGTTGAATATGAAGAGGGAGATTGCCTCCGTATACTTCCATGCCATCATGAATTCCATCTAACATGTGTAGACAAATGGCTAAAGGAGATTCACAGgtattcatcctcttatttaa-caatgagcattctttat--gtttgtgaacag---tgggggtccttttttatccacatctaggaaaaagaaactgctgaatcagca

upper sequence: LOC_Os05g32350.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G060999_T01 (Zea mays), 5'ss of exon 5
GCCTTGTTGAATATGCCGAGGGAGACTGTGTCCGTATTCTTCCATGCAATCATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatggattaatctaaataatttataatttgcataagtaaatgaacagaactgcggtcaacatgctattgttacctctttatgtcagagctctatag-------
|||||||||||||||  |||||||| ||| | ||||| ||||||||| |||||||||||||||||||||| |||||||||||||| || ||||| |||||||||      | ||     ||  ||| |||||  | |     ||  |  |     |   ||  ||||||||  |||   |   || || |||||   | |       
GCCTTGTTGAATATGAAGAGGGAGATTGTCTTCGTATACTTCCATGCCATCATGAATTTCATCTAACATGTGTAGATAAATGGTTAAAGGAGATTCACAGgtat------tcaaatcgtattctttttaattcacttctaggaaaaagaaactacgtaatctgcatgctataattagggccggatatc-gagctagcttggctcgtt

upper sequence: LOC_Os05g32350.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA01G35490.1 (Glycine max), 5'ss of exon 5
GCCTTGTTGAATATGCCGAGGGAGACTGTGTCCGTATTCTTCCATGCAATCATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatggattaatctaaataatttataatttgcataagtaaatgaacagaactgcggtcaacatgctatt-gttacctctttatgtcagagctctatag--
||||||| || ||||  || |||||| |  | ||  |||| || ||  ||||||||||||||  |||||| ||||| || ||| |||| ||||| |||||||||| ||| |  |   |  |   |     |||| |||| || |||   | ||      |  | ||   |||  || |     | | || ||    ||| |  
GCCTTGTGGAGTATGAGGATGGAGACAGCATGCGAGTTCTGCCTTGTCATCATGAATTTCATACAACATGTGTAGACAAGTGGCTGAAGGAGATTCACAGgtatg-tgggtatagggagttgggtgtccttttggataattatatggctaaaaaca-aatttatataaaatttattgctatggtgtatc-gattcatatcggg

upper sequence: LOC_Os05g32350.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA09G35060.1 (Glycine max), 5'ss of exon 7
GCCTTGTTGAATATGCCGAGGGAGACTGTGTCCGTATTCTTCCATGCAATCATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatggattaatctaaataatttataatttgcataagtaaatgaacagaactgcggtcaacatgctattgttacctctttatgtcagagctctatag-
||||||| || ||||  || |||||| |  | ||  |||| || ||  ||||||||||||||  |||||| ||||| || ||| |||| ||||| |||||||||| ||| |  |   |  |         |||| |||| || |||   | ||           ||   |   ||||  || |     |    |  |||  
GCCTTGTGGAGTATGAGGATGGAGACAGCATGCGAGTTCTGCCTTGTCATCATGAATTTCATACAACATGTGTAGACAAGTGGCTGAAGGAGATTCACAGgtatg-tgggtatagggagttgggagtccttttggataactatatggctaaaaacttcaaatctatataaaatttactgctgtggtgtatcaattcatatc

upper sequence: LOC_Os05g32350.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv02s0087g00420.t01 (Vitis vinifera), 5'ss of exon 5
GCCTTGTTGAATATGCCGAGGGAGACTGTGTCCGTATTCTTCCATGCAATCATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatggattaatctaaataatttataatttgcataagtaaatgaacagaactgcggtca-acatgctattgttacctctttatgtcagagctctatag-
||||||| || ||||  || ||||||    | ||  |  | || ||| ||||||||||||||   ||||| ||||| || ||| | ||||||||||||||||||| |||   | |     |    |  ||| |           |  |||| |       || | ||||    |        || | | |  | | |||   
GCCTTGTGGAGTATGAGGAAGGAGACAACATGCGGGTGTTACCTTGCCATCATGAATTTCATAGGACATGTGTAGACAAGTGGCTAAAAGAGATACACAGgtatg-tggtcaatttggcgtctccttgaatctttgatgtctcgtttacagtataatatgcacatatgcacgggcgtgtaagttctattatcg-tttatctc

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|58600887|gb|CK011415.1|CK011415
EST:     CATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAG                         GGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCAT
genomic: CATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatgga ... tttctttcagGGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCAT
EST: gi|88289627|gb|CI522760.1|CI522760
EST:     CATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGG                         GGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCA
genomic: CATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACA-Ggtatgatgga ... tttctttcagGGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCA
EST: gi|87029174|gb|CI276442.1|CI276442
EST:     CATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAG                         GGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCAT
genomic: CATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatgga ... tttctttcagGGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCAT
EST: gi|89187239|gb|CI047306.1|CI047306
EST:     AGAGATACACAG                         GGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCAT
genomic: AGAGATACACAGgtatgatgga ... tttctttcagGGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCAT
EST: gi|86426220|gb|CI071317.1|CI071317
EST:     CATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAG                         GGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCAT
genomic: CATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatgga ... tttctttcagGGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCAT

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: 69 (upstream exon), 71 (downstream exon)
Score: 7

GCCTTGTTGAATATGCCGAGGGAGACTGTGTCCGTATTCTTCCATGCAATCATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatgga ... tttctttcagGGTTTGTCCACTTTGTCGTGGTGATGTCTGCAGATCCAATGCATCAGGCATTGGAAAAACCACATGATCTTCTCTTCTGTGAGAAAAATGGAGCTTCTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTGTTGAATATGCCGAGGGAGACTGTGTCCGTATTCTTCCATGCAATCATGAATTTCATCTAACATGCGTAGATAAATGGTTGAAAGAGATACACAGgtatgatggattaatctaaataatttataatttgcataagtaaatgaacagaactgcggtcaacatgctattgttacctctttatgtcagagctctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA