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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgttttcttctatcatcacaatttgaaaatagaatttagattggtgttcattctttacttgtatttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAAATCCTCAAATGCTGAACCCCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g50480.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 9
gtaatttgttttcttctatcatcacaatt-tgaaaatagaatttagattggtgttcattctttacttgtatttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAA---ATCCTCAAATGCTGAACCCCCAG
|||||  ||  ||||||||  |||||| | |  |  || ||| | | | ||| || |||| | |||| ||||||| ||||| ||||||||||| || ||||| ||||||||||| ||||||||||||||  | ||||| || ||||| ||||||||   ||||||||||| ||| || |   
gtaatgagt--tcttctattgtcacaaatatctacttataatgtggctaggtattaattcatcacttatatttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC---

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 9
gtaatttgttttcttctatcatcacaatt-tgaaaatagaatttagattggtgttcattctttacttgtatttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAA---ATCCTCAAATGCTGAACCCCCAG
|||||  ||  ||||||||  |||||| | |  |  || ||| | | | ||| || |||| | |||| ||||||| ||||| ||||||||||| || ||||| ||||||||||| ||||||||||||||  | ||||| || ||||| ||||||||   ||||||||||| ||| || || |
gtaatgagt--tcttctattgtcacaaatatctacttataatgtggctaggtattaattcatcacttatatttttgcaggagGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTG

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 9
gtaatttgttttcttctatcatcacaa-tttgaaaatagaatttagattggtgttcattctttacttgtatttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAA---ATCCTCAAATGCTGAACCCCCAG
|||||  ||  ||||||||  |||||| |||  |  || ||| | | ||||     |||| | |||| | ||||| ||||| ||||||||||| || ||||| ||||||||||||||||||||||||||  | ||||| |||||||| ||||||||   ||||||||||| |||||| |   
gtaatgagt--tcttctattgtcacaagtttctacttaaaatatggcttggga---attcatcacttatgtttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC---

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------------------------------gtaatttgttttctt-------ctatcatcacaatttgaa-aatagaattta-gattggtgttcattctttacttgtatttt-tacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAAATCCTCAAATGCTGAACCCCCAG-
                                      | ||| |  |||| |        ||| |  |||  ||||| | |    |||| ||||  |    |  |   | | | |   | ||||||| ||||||||||||||||| || ||||| || || |||||||| || || || || |  || |||||  |  | ||| |     ||||||     | || 
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGG-TGGCGAGC

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
------------------gtaatttgttttcttct-----atcatca-------caatttgaaaat---agaatttagattggtgttcattctttacttgtattttt---acagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAAATC---CTCAAATGCTGAACCCCCAG
                     |||| || |||  |     || ||||        ||||| ||||    ||||| |    |  | |   || ||  ||  | |  |    |||||||||||||||||| || |||||||||||||| || ||||||||||| ||  | ||||   | |||||  | || |||||     | ||   ||| || |   
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC---

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|58663537|gb|CK052223.1|CK052223
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|58695799|gb|CK084486.1|CK084486
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|58693865|gb|CK082552.1|CK082552
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|45244957|gb|AB118181.1|AB118181
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|58657583|gb|CK046263.1|CK046263
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|58596192|gb|CK006720.1|CK006720
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|29664693|gb|CB660968.1|CB660968
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         -A---CTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|58682481|gb|CK071168.1|CK071168
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|218492308|gb|FG946716.1|FG946716
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|15008682|gb|AU223070.1|AU223070
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|58670270|gb|CK058956.1|CK058956
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|58597742|gb|CK008270.1|CK008270
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|29689390|gb|CB685665.1|CB685665
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|58604363|gb|CK014891.1|CK014891
EST:     GCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: GCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|58601534|gb|CK012062.1|CK012062
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
EST: gi|12622980|gb|AU173193.1|AU173193
EST:     TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAG                         GAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA
genomic: TGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAA

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: 212

TTATGATGCTCTCCATGGTGTTGCTGGGACTTACGCAACACGCATCTTTGTGGAAGAGCTTGGTGCTGCTGAAAGCTCATTGTTGAACTGTGTTCCGAAGgtaatttgtt ... atttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAAATCCTCAAATGCTGAACCCCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatttgaaaatagaatttagattggtgttcattctttacttgtatttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAAATCCTCAAATGCTGAACCCCCAG
                                            tattttt  CT-rich tract
        aaaatagaatttagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgttttcttctatcatcacaatttgaaaatagaatttagattggtgttcattctttacttgtatttttacagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAAATCCTCAAATGCTGAACCCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG