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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACGCCGGCAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcactaaacaccccaagaattatgtagttgctccttttgtttcttaaccaaaatattatactgctagtagtagcatgtgcttggatgggctttgag...

Basic information

species Oryza sativa
transcript LOC_Os03g18180.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18180.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G094388_T01 (Zea mays), 5'ss of exon 3
CACGCCGGCAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcactaaacaccccaag--aattatgtagttgctcctt-ttgtttcttaaccaaaatattatactgctagtagtagcatgtgcttggatgggctttgag
||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||| || || || |||||||| ||||||||| |||||     |||  |    |  |   |  ||   |||| |||  |||   |  |  ||  |  |||| | |  ||  ||||  | | |      |||| 
CACGCGGGGAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGCGAGCTCAAAGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcacctcgaaccatatcttacctgcctctttatcccttcttgcatctgttcgtagctagcagcctgc-actgttacaatgt-ttggtacctctgttga-

upper sequence: LOC_Os03g18180.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G078933_T01 (Zea mays), 5'ss of exon 3
CACGCCGGCAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcactaaacaccccaagaattatgtagttgctccttt----tgtttcttaaccaaaatattatactgctagtagtagcatgtgcttggatgggctttgag
||||| || |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||| || || || |||||||| ||||||||| |||||  |  ||       | |   |  |  |||||||       ||| |||| |  |  || |||||  | || ||    || | |   | |   |||| 
CACGCAGGGAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGTGAGCTCAAGGAGGAGATGTTTGCTATCCGTTTTGGATCTGTCGAGAgtgagcacccataacatatcctacttctttatccctcctttgcatctgttcataactagcagcttgtactgtca-taatatttggtacctctgttga--ttga-
















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|396941311|gb|HO188520.1|HO188520
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|58604270|gb|CK014798.1|CK014798
EST:     CGGCGAGCTCGAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|163929481|gb|EG713448.1|EG713448
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|89195003|gb|CI051116.1|CI051116
EST:     GATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: GATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|300216294|gb|HO088079.1|HO088079
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|58676147|gb|CK064834.1|CK064834
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|58680025|gb|CK068712.1|CK068712
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|300215615|gb|HO088241.1|HO088241
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|58678167|gb|CK066854.1|CK066854
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|87031265|gb|CI259845.1|CI259845
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|86421213|gb|CI057202.1|CI057202
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|86518603|gb|CI158809.1|CI158809
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|300216238|gb|HO088023.1|HO088023
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|15851407|gb|BI799683.1|BI799683
EST:     CGGCGAGCTCAAGGAGGAAATGTTCCCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGA-CAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|66928667|gb|CX115515.1|CX115515
EST:     CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: CGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
EST: gi|66913167|gb|CX100015.1|CX100015
EST:     TTTGGATCCGTCGAGA                         ACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA
genomic: TTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAA

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), 67 (downstream exon)
Score: 29

CACGCCGGCAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcacta ... tttgtttcagACTGCAAGAAGTTCAGGGAGATGGTAGAAGAGATTGCTGAGCAGCAAGGAAAGAACGAGGAGAAAGAAAATGAGGAAGTCTCCTCTACTGCAGGGTTGGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACGCCGGCAGCGACAAGTCGTGCGTGTGGCACGCGCTGGACTTCGCCGACGGCGAGCTCAAGGAGGAAATGTTCGCCATACGCTTTGGATCCGTCGAGAgtaagcactaaacaccccaagaattatgtagttgctccttttgtttcttaaccaaaatattatactgctagtagtagcatgtgcttggatgggctttgag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatggg