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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttaactgagctattgaattggagccactccacttttgttcagtttctcttccatatagtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC

Basic information

species Oryza sativa
transcript LOC_Os02g01490.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G429241_T01 (Zea mays), 3'ss of exon 11
--gtactttaactgagctattgaattggagccactcca----cttttgttcagtttctcttccatata-gtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC
   |  ||| |||| | ||| ||| ||||    |||||     |||| ||||  |  ||||   |||| | || || ||   |  ||||||   | |||  ||||||| ||||||||| | || ||||| ||||||||||| |||||  | ||||| |||||||||||||||||||   |||||||||| ||||||||||| ||||
gtatttttttactgggttat-gaaatggacaatctccagttttttttcttcatctcttcttttctatatgcaaggccaac-ttatgatcctatttctgttctgaagGCAAAATTAGGGGATCAGAACAAATTTTACTATGATGAAAAATTGAAGCGGTGGGTGGAGGAAGGTGCTGCTGTTCCTGCCGAAGAGCCTCCTCTTCCTC

upper sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G163277_T01 (Zea mays), 3'ss of exon 11
gtactttaa----ctgagctattgaattggagccactcca---cttttgttcagtttctcttccatata-gtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC
||| ||| |    ||||| |||  ||   ||    |||||   |||||   ||  || |||    |||| | || |  ||   |  ||||||   | |||  ||||||| ||||||||| | || ||||| ||||||||||| |||||| | ||||| |||||||| |||||||||| | |||||||||||||||||||||| ||||
gtatttttatttactgagttatgaaa--agactatctccagttcttttccccatcttgtctcttctatatgcaatgtcaaccttaggatcctatttctgttctgaagGCAAAATTAGGGGATCAGAACAAATTTTACTATGATGAAAAGTTGAAGCGGTGGGTGGAAGAAGGTGCTGTGGTTCCTGCCGAGGAGCCTCCTCTTCCTC

upper sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA01G41800.1 (Glycine max), 3'ss of exon 13
gtactttaactgagctattgaattggagccactccacttttgttcagtttctcttccatatagtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC
    | ||| | |    || | ||        | |||    || |  ||     |    || || ||     || | |  ||    |||| |   | |||||||||| ||  |  |||||||||| || ||||| || ||||| ||| |||||||||| |||||||||||  |||| || || ||  || ||   |  |
---gtataattaattgttttattttctttttattcacaacagtgc--ttctgactgtgcatggtcaaatggttatttat-tctactctatat---gtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAAGAAGGTGCTGAACTTCCAGCTGAAGAAGCTGCTGCTCTGC

upper sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 16
gtactttaactgagctattgaattggagccactccacttttgttcagtttctcttccatatagtaaagctaatactgagatccttcc-tatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC
    | ||| | || | ||  |||        ||   || |   ||      ||||    |      | | | |  |   |  |||   |     || |||||||||| ||  |  |||| ||||| || ||||| || ||||| ||| ||||||||||||||||||||||  |||| || || ||  || ||   |   
---gtataatt-agttgttttatt-------ttctttttattcacaacagtgcttctgactgtgcctgttcaaatggttcttgttctacactatatgtagGCTAAATTGGGTGACAAAAATAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTGCTGCTCTGA

upper sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA11G03590.1 (Glycine max), 3'ss of exon 17
gtact-ttaactgagctattgaattggagccactccacttttgttcagtttctcttccatatagtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC
|||   |||  ||   ||||   ||       | ||||  |  ||| | || |      |  | |    || || ||      ||   |||||     |||||||||| ||  |  |||||||||| || ||||| || ||||| ||| ||||||||||||||||||||||  |||| || || ||  || ||   |  |
gtataattagttgttttattttctttttatt-caccacagtgcttctgattgtgcctgtttaaatggttcttattcta-----ctctatatgt-----agGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC

upper sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 15
gtact-ttaactgagctattgaattggagccactccacttttgttcagtttctcttccatatagtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC
|||   |||  ||   ||||   ||       | | ||  |  ||| | || |      |  |||    || || ||   |  ||   |||||     |||||||||| ||  |  |||||||||| || ||||| || ||||| ||  ||||||||||||||||||||||  |||| || || ||  || ||   |  |
gtataattagttgttttattttctttatatt-cacaacagtgcttctgattgtgcctgtttaagtggttcttattct---actctgtatatgt-----agGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAAAGATGGGTGGAGGAAGGTGCTGAACTTCCAGCTGAAGAAGCTGCTGCTCTGC

upper sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 12
gtactttaactgagctattgaatt--ggagccactccacttttgttcagtttctcttccatatagtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC
||| |||   || |||| |   ||  | |   |  |  | | | |  | |     ||  |  | || |  | |||| |   || ||   |   |  ||||||| ||| ||||  |  | || || ||||| ||||| |||||||| ||||||||||| ||||||||| ||||  ||||  | || ||  |  |  | || |
gtagtttc-ttgtgctagttgtttctgtaaatagactccctgtatataatcatctttttac-tggtgat-caaatatttt-atgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC

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|58610863|gb|CK038575.1|CK038575
EST:     GCTCCACACTACAGAAGACAATGGGATTTGTTTCAAAATCCCACCGGCAG                         GCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGA
genomic: GCTCCACACTACAGAAGACAATGGGATTTGTTTCAAAATCCCACCGGCAGgtactttaac ... tgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGA
EST: gi|66924353|gb|CX111201.1|CX111201
EST:     GCTCCACACTACATAAGACAATGGGATTTGTTTCAAAATCCCACCGGCAG                         GCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGA
genomic: GCTCCACACTACAGAAGACAATGGGATTTGTTTCAAAATCCCACCGGCAGgtactttaac ... tgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGA
EST: gi|86851109|gb|CI311327.1|CI311327
EST:     GCTCCACACTACAGAAGACAATGGGATTTGTTTCAAAATCCCACCGGCAG                         GCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGA
genomic: GCTCCACACTACAGAAGACAATGGGATTTGTTTCAAAATCCCACCGGCAGgtactttaac ... tgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGA

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: 56 (upstream exon), 73 (downstream exon)
Score: 14

CACACAGAGTACTGCTCCAGGATCTGGTAGTTCACGCTTTGGTTGGTTAGGCTCCACACTACAGAAGACAATGGGATTTGTTTCAAAATCCCACCGGCAGgtactttaac ... tgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttctcttccatatagtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC
                      agctaat  putative branch site (score: 14)
                                    tccttcctatgtctt  putative PPT
             atatagtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttaactgagctattgaattggagccactccacttttgttcagtttctcttccatatagtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC