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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtctctaccacctaaaagcggagtcgtccatacgctccttcccacgcgtcacaaagcacacaagcactgccttctaggcctgaaaataacaga...

Basic information

species Oryza sativa
transcript LOC_Os03g62700.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62700.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G071877_T01 (Zea mays), 5'ss of exon 6
TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtctctaccacctaaaagcggagtcgtccatacgctccttcccacgcgtcacaaagc-acacaagcactgccttctaggcctgaaaataacaga
 ||||| ||||| ||||| || || |||||||||||  ||||||||||||||||||| || |||||||||||||| ||||| |||||| ||||||| |||||||||| | | | | | || | |  ||||   |   | |     | |      || | |  || |    |  |||  | |     |   || ||| || |
CGATGTCTACAGCTTTGGCGTGGTCCTTTTGGAACTTTTGACTGGAAGGAAACCAGTAGATCACACAATGCCTCGAGGACAACAAAGTTTAGTCACATGGgtaagttatttttgctaacttacattggaga-atggttgcttatgtgctgtacagtaatactgctattggaatactaacatggcttcgcaaatatagcata

upper sequence: LOC_Os03g62700.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G001668_T01 (Zea mays), 5'ss of exon 6
TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtctctaccacctaaaagcggagtcgtccatacgctccttcccacgcgtcacaaagcacacaagcactgccttctaggcctgaaaataacaga-
|||||| ||||| |||||||| ||||||||||||||  ||||||||||||||||||| || |||||||||||||| || || |||||| ||||||| |||||||||| | |     || || |   |     |            ||     ||   | | |  ||    ||  | |   |  ||| | | || || ||  
TGATGTCTACAGCTTTGGTGTGGTTCTTTTGGAACTTTTGACTGGAAGGAAACCAGTAGATCACACAATGCCTCGAGGTCAACAAAGTTTAGTCACATGGgtaagttattttgctaacttacattggagaatggttgcttatgtgttgttgtgcagta-atactactattgccatactgacatggcttcacaaaaatagcc

upper sequence: LOC_Os03g62700.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagt-tgtctctaccacctaaaagcggagtcgtccatacgctccttcccacgcgtcacaaagcacacaagcactgccttctaggcctgaaaataacaga---------
|||||| || ||||||||||| |||||| | || || || || ||||| ||||| || ||||| || |||||| | |||||||| ||||| ||||| ||||| ||| |||||     | || | | |  |  ||| | | |     |||   |   | |||  |       ||  |   |  |  |  ||| | | | |           
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgc-tgctgcttttcaatcatttaacactggttgtcggccataggtattttgt-tgacattgatatttttttgtag

upper sequence: LOC_Os03g62700.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G44210.1 (Glycine max), 5'ss of exon 7
TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagt-tgtctctaccacctaaa----agcggagtcgtccatacgctccttcccacgcgtcacaaagcacacaagcactgccttctaggcctgaaaataacaga
|||||| || ||||||||||| |||||| | || || || ||||| || ||||| || ||||| || |||||| | |||||||| ||||| ||||| ||||| ||| ||   ||   ||  | |    | ||  |  ||   |       || ||||  ||    |  || | |     ||  |  ||    |     |   || 
TGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgctgcttaaactcatacctcatcgctgctgtttttcaatcatttaccactggttgtcagccatagatattttgt-tgatattgatattttttgtag-

upper sequence: LOC_Os03g62700.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G59350.1 (Arabidopsis thaliana), 5'ss of exon 4
TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtctctaccacctaaaagcggagtcgtccatacgctccttcccacgcgtc-acaaagcacaca-agcact-gccttctaggcctgaaaataacaga
|||||| || ||||||||||| || |||||||| ||| ||||||| |||||||| || || || || |||||||| || || |||||||| || |||||||| |||       ||||  |          |  |    |   || | |   ||  |  ||  |     |   ||| | ||| |||   | | |          
TGATGTTTATAGTTTTGGTGTGGTGCTTTTGGAGCTCTTGACTGGTAGGAAACCCGTCGATCATACGATGCCTCGTGGTCAACAAAGTCTTGTTACTTGGgttagt-actaaaaccatgttgctttaattttctgaggataatcttactttcgaatttactgattgttcttggcatttgccgtcttaacttcag---------

upper sequence: LOC_Os03g62700.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 5'ss of exon 5
TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtctctaccacctaaaagcggagtcgtccatacgctccttcccacgcgtcacaaagcacacaagcactgccttctaggcctgaaaataacaga
|||||| ||||||||||| || || ||||||||||| || || || || ||||| || || || || |||||||| || || || ||||| ||||||||||||      ||  ||   || ||   |      ||  |  |   || || |  | |  |   |   | ||    | |  | ||   || | |   |    
TGATGTTTACAGTTTTGGAGTTGTGCTTTTGGAACTTCTTACCGGGAGAAAACCGGTTGATCATACTATGCCTCGTGGTCAACAGAGTCTTGTCACTTGGgta------cttaacttacttaatttgactctttctttctgagactaccaaatcttttcttggt-tataac--tttctctgtaaatctaatatccag---

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|86505201|gb|CI147834.1|CI147834
EST:     AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
genomic: AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
EST: gi|218478503|gb|FG957072.1|FG957072
EST:     AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
genomic: AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
EST: gi|25806626|gb|CA762587.1|CA762587
EST:     AGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
genomic: AGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
EST: gi|86496614|gb|CI139247.1|CI139247
EST:     AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
genomic: AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
EST: gi|33681453|gb|CF309692.1|CF309692
EST:     AATGCCTCGGGGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
genomic: AATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
EST: gi|58608400|gb|CK036433.1|CK036433
EST:     AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
genomic: AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
EST: gi|89175450|gb|CI042471.1|CI042471
EST:     AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
genomic: AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
EST: gi|33681452|gb|CF309691.1|CF309691
EST:     AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGGTGTAGATCCTAG
genomic: AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATG-TGTAGATCCTAG
EST: gi|87004534|gb|CI300856.1|CI300856
EST:     AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
genomic: AACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
EST: gi|86415039|gb|CI069442.1|CI069442
EST:     GGACAGCAAAGTCTAGTCACTTGG                         GCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
genomic: GGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG
EST: gi|87027317|gb|CI269992.1|CI269992
EST:     TAGTCACTTGG                         GCTACTCTTAGATTAAGCGAAGACAAGTTCAAACAATGTGTAGATCCTAGG
genomic: TAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGG

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: 75 (upstream exon), 71 (downstream exon)
Score: 29

TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtc ... ttctctccagGCTACTCCTAGATTAAGCGAAGACAAGGTCAAACAATGTGTAGATCCTAGGTTAAAGAGTGAATATCCTCCAAAGGGAGTTGCTAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACAATGCCTCGGGGACAGCAAAGTCTAGTCACTTGGgtaagttgtctctaccacctaaaagcggagtcgtccatacgctccttcccacgcgtcacaaagcacacaagcactgccttctaggcctgaaaataacaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cggagtcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa