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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAACAAATGAAGAGAATTGGCAATGAGCTGGATACTGTTCACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccatccctctctcttccctctgcgtgcgcttgtgcttttgcatgtccagcagtacctgaaatttgaaatccttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g25390.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g25390.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G330650_T02 (Zea mays), 5'ss of exon 7
ACAGAACAAATGAAGAGAATTGGCAATGAGCTGGATACTGTTCACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccatccctctctcttccctctgcgtgcgcttgtgcttttgcatgtcca-gcagtacctgaaatttgaaatc-----cttgcag
||||| ||||||||||||||||| |||||||| |||||||| ||||| ||  | ||||| |||||||| || ||||| |||||||| || |||| || |||    || ||||   |     | |   |    | |   ||| |  || ||| |  |||||| || ||  |      ||||||
ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccc---tctttctcagtctctgacatatacaaacggtga-gcacgcacaagcactgactgaaagttaaacacatgattttgcag
















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|30227163|gb|CB965055.1|CB965055
EST:     TTGGGCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: TTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|27921131|gb|CB096939.1|CB096939
EST:     ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|30228758|gb|CB966648.1|CB966648
EST:     TTGGGCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: TTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|88509241|gb|CI436747.1|CI436747
EST:     AGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: AGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|30228750|gb|CB966640.1|CB966640
EST:     TTGGGCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: TTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|15008275|gb|AU222663.1|AU222663
EST:     ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|15855989|gb|BI808801.1|BI808801
EST:     ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTTGCC-TCAG                         GTTGCAACTGAC-AATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|88969544|gb|CI383054.1|CI383054
EST:     CTGGTGAAAGAGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: CTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|87015371|gb|CI275561.1|CI275561
EST:     ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|89186178|gb|CI048047.1|CI048047
EST:     ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|86594199|gb|CI262427.1|CI262427
EST:     ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|88262856|gb|CI364434.1|CI364434
EST:     AGCCAGCTGGTGAAAGAGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: AGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|86864804|gb|CI344294.1|CI344294
EST:     AGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: AGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|88275141|gb|CI395745.1|CI395745
EST:     GATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: GATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|88827221|gb|CI777786.1|CI777786
EST:     ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: ACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
EST: gi|14980927|gb|BI305605.1|BI305605
EST:     TTGGGCGTCAG                         GTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT
genomic: TTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGT

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), 66 (downstream exon)
Score: 25

ACAGAACAAATGAAGAGAATTGGCAATGAGCTGGATACTGTTCACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccat ... atccttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGAACAAATGAAGAGAATTGGCAATGAGCTGGATACTGTTCACTTTTCGTTAAAGAAGGCTAGCCAGCTGGTGAAAGAGATTGGCCGTCAGgtacccccatccctctctcttccctctgcgtgcgcttgtgcttttgcatgtccagcagtacctgaaatttgaaatccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA