Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAAGTTGTTCTGTGATACAGACTATCCAGACAGACCACCTACTGTTCGATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtccacttgctttcctttaagctaaagtagttggtgaatcattttattggcgtagtacttacaaggagctactttctag

Basic information

species Oryza sativa
transcript LOC_Os03g50440.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G090172_T02 (Zea mays), 5'ss of exon 3
GTTGAAGTTGTTCTGTGATACAGACTATCCAGACAGACCACCTACTGTTCGATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtccacttgctttcctttaagct------------aaagtagttggtgaatcattttattggcgtagtacttacaaggagctactttctag
 || ||| |||| |||||||| || |||||||| | |||||| || || |||||||||||||| ||||||||| |||| ||||| |||||||||||| |||||| ||| || ||   || |||  |||             |  | | ||   |||| || |||  |||  | | ||||    |  ||  |||||||
ATTAAAGCTGTTTTGTGATACGGATTATCCAGATAAACCACCGACAGTCCGATTCCAGACTCGGATCAATATGACATGCGTGAACCAAGAAACTGGATTGgtacttgtgcatttttgtttcttacagcgtgcaacctgccaagggcaatttacgaatgatatta--ggcccattgcttagctagcact-ttttctag

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G022859_T01 (Zea mays), 5'ss of exon 3
GTTGAAGTTGTTCTGTGATACAGACTATCCAGACAGACCACCTACTGTTCGATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtccacttgcttt---cctttaagct-----------aaagtagttggtgaatcattttattggcgtagtacttacaaggagctactttctag
||| ||| |||| ||||||||||| |||||||| | |||||| ||||| |||||||||||||| ||||||||| |||||||||| |||||||||||| ||||||  || |  ||  |||    |||  ||||           || | | ||  ||||| ||  ||  ||| || ||||||    |  |   |||||||
GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgctttttttttgtttcttatagcttgcaacctaccaaggcaatttatgaatgatagta--ggcctattacttaactagcacc-ttttctag
















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|15852518|gb|BI805314.1|BI805314
EST:     AAACTGGAATG                         GTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
genomic: AAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
EST: gi|27545659|gb|CA763865.2|CA763865
EST:     GATTCCAGACTCGAATCAATACGTCATGTGTGAATCAAGAAACTGGAATG                         GTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
genomic: GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
EST: gi|88242402|gb|CI242251.1|CI242251
EST:     GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATG                         GTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
genomic: GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
EST: gi|88200708|gb|CI200558.1|CI200558
EST:     GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATG                         GTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
genomic: GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
EST: gi|86845255|gb|CI340364.1|CI340364
EST:     AATATGTCATGTGTGAATCAAGAAACTGGAATG                         GTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
genomic: AATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
EST: gi|88415272|gb|CI586478.1|CI586478
EST:     GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATG                         GTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
genomic: GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
EST: gi|58592031|gb|CF990339.1|CF990339
EST:     GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATG                         GTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
genomic: GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
EST: gi|89194551|gb|CI116988.1|CI116988
EST:     GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATG                         GTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
genomic: GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
EST: gi|58691622|gb|CK080309.1|CK080309
EST:     GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATG                         GTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA
genomic: GATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACA

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: 70 (upstream exon), 74 (downstream exon)
Score: 44

GTTGAAGTTGTTCTGTGATACAGACTATCCAGACAGACCACCTACTGTTCGATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtcc ... tactttctagGTTGAACCAAGTCTATTCCCCATGCTTGGTAACTGGCAAAGAGAACATACAATGCAAGACATCCTGATCGGCTTAAAAAAGGAGATGTCTGCTCCTCAGA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAAGTTGTTCTGTGATACAGACTATCCAGACAGACCACCTACTGTTCGATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtccacttgctttcctttaagctaaagtagttggtgaatcattttattggcgtagtacttacaaggagctactttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA