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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaaagctcttttggttaggattattctgttcgtggtaaatttcatgttgtttttttttttttgggtacttgactgctgtgttgttactggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA

Basic information

species Oryza sativa
transcript LOC_Os09g24540.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
-tttaaagctcttttggttaggattattctgttcgtggtaaatttcatgttgtttttttttttttgggtacttgactgctgtgttgttactggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA
   |  || |            | | || |||   || | |  ||  || |      |        | |  || |    | ||||||  |||  | | |||||||||||||| |||| |||||||| |||||||||||||||||||| ||||||||||||||||| ||| || | || |||||||| || |||||||| ||
aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtc-ctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA

upper sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 2
-tttaaagctcttttggtt----aggattattctgttcgtggtaaatttcatgttgtttttttttttttgggtac-ttgac-tgctgtgttgttactggtt--tttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA
 |  |||  | |     |        |  ||| |   | || | | || | | |  |  ||| | ||      || ||||| |  | | | | |  |  ||  |||||||||||||  | || || ||||| ||||| |||||||||||||| ||||||||| |||||||||| ||| | | ||| || ||||||||||| || || ||
gtaaaaaaatttccccatccacggataccattgtaaccatgattagtt-cttttcatagtttgtcttagaatgacattgacatcttttatggctttttattcctttcagCTAGGCATATCCTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGA

upper sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 2
-tttaaagctcttttggttaggattattctgttcgtggtaaatttcatgttgtttttttttttttgggtacttgactgctgtgttgttactggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA
 |  |||  |       |         | |   | || | ||||   | ||  |  ||| | || |  |     | |  | ||   ||        |||||| |||||  |  | || ||||| ||||| |||||||||||||| ||||||||| |||||||||| ||| |   |||||| || |||||||| || || ||
gtagaaaatttcccccat--------ctgtaaccatgattaattc--ttttcatagtttgtcttagaatgacatatttttttggctttttattccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA

upper sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------ttta-----aagctcttttggttaggattattctgttcgtggtaaatttcatgttgtttttttttttttgggtacttgactgctgtgttgttactggttttt----cagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA
                                       || |     ||    |  |||| |  |    |   | |        | | |     ||| | ||  |       | | |  |     |    | | ||||||    |||| || || ||  |||||||||||||||| |||||||| || || ||||| |||||||||||||| ||||||  |||||| |||||||| |||||||| ||
gtgtgttttttggattcgtttctgtgcctgttacctttgttcatgagtaaaaaatactggtaaacaaatatggatccaaaagttctcttacaacttttgtattagtacaatagcattaaagtcaaatctccaattgtttttgtttcagCAAGACATGTTTTGTGCGAGAAGCAAGGAAAGATCAACGAGGCCTACAAAAAGTTGCAGGATGGTTGGTTGAGCAACGGAGACAAGGTTCCTCCTGCTGA

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|88328328|gb|CI651339.1|CI651339
EST:     AAGGGCGG-ATAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: AAGGGCGGCA-AGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|86421356|gb|CI057345.1|CI057345
EST:     CAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: CAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|11565000|gb|AU165636.1|AU165636
EST:     AA-GGCGGCAAGTCCGCCGACGGGCNTCGGCACTTGCACNTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: AAGGGCGGCAAGTCCGCCGAC-GGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|87032537|gb|CI266177.1|CI266177
EST:     GTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: GTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|89162824|gb|CI099714.1|CI099714
EST:     CGCCGACGGCCTCGGCACCTGCACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: CGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|88988530|gb|CI037766.1|CI037766
EST:     AAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCCAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: AAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|86529352|gb|CI169558.1|CI169558
EST:     TCCGCCGACGGCCTCGGCACCTGCACGTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: TCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|117222380|gb|CT845828.1|CT845828
EST:     CAAGGGCGGCAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: CAAGGGCGGCAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|87027147|gb|CI278179.1|CI278179
EST:     CAAGGGCGGCAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: CAAGGGCGGCAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|88212503|gb|CI212143.1|CI212143
EST:     CGACGGCCTCGGCACCTGCACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: CGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|86897009|gb|CI317442.1|CI317442
EST:     CCGACGGCCTCGGCACCTGCACCTACGTCAAAG                         GTAGGCACTTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAAA
genomic: CCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|87031863|gb|CI272564.1|CI272564
EST:     CACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: CACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|3061265|gb|C91897.1|C91897
EST:     CAAGGGCGGCAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
genomic: CAAGGGCGGCAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA
EST: gi|58693353|gb|CK082040.1|CK082040
EST:     CAATGGCGGCAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAG                         CTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCGATGAAGCTTACAAGA
genomic: CAAGGGCGGCAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGA

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), 75 (downstream exon)
Score: 96

GGCTCGTCCGGCGGCGATGACGCCGGCGGCGGCGGCAAGGGAGGCAAGGGCAAGGGCGGCAAGTCCGCCGACGGCCTCGGCACCTGCACCTACGTCAAAGgtatctccag ... ggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttgtttttttttttttgggtacttgactgctgtgttgttactggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA
                       acttgac  putative branch site (score: 96)
                                               tttttc  putative PPT
      ttttttttttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaaagctcttttggttaggattattctgttcgtggtaaatttcatgttgtttttttttttttgggtacttgactgctgtgttgttactggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - tcttttg
- - - - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgctg