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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactaccaaatgatttgaattatgaatatttcctgatcattattaattgcccgcatccaacttctggtaaaaaaatatgttctccttaaattccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTTCCCGTGTGGTGCAACAAAGATGACAGTGTCAAGCTCCCCTTCTGCCAAA

Basic information

species Oryza sativa
transcript LOC_Os01g58114.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g58114.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G139374_T02 (Zea mays), 3'ss of exon 6
-cactaccaaatg-atttgaattatgaatatttcctgatcat-tattaattgcccgcatccaacttctggtaaaaaaatatgttctccttaaattccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTTCCCGTGTGGTGCAACAAAGATGACAGTGTCAAGCTCCCCTTCTGCCAAA
  |    |   || |||||| ||    |   |    | | ||  |  |  |    ||      ||| |  |    || | | ||  ||  | |||   ||||||||||||||||||| | |||||||||||||||| ||||   ||| || ||||| | |||||||||||| ||||||  ||| ||||| ||||| ||||| |
aaagagtcttgtgcatttgagtttctgacggtagaggcttatacagaagctattggcgga-gtcttgtctttctcaattctatttcccccatattt--tgcagATAAAAGATGCTTATATCCTCAACTTTTTTGAGGACAACTCGACCCGACTTCCGGAGTGGTGCAACAAGGATGACGATGTGAAGCTTCCCTTTTGCCAGA

upper sequence: LOC_Os01g58114.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G54870.1 (Arabidopsis thaliana), 3'ss of exon 6
cactaccaaatgatttgaatt-atgaatatttcctgatcattattaattgcccgcatccaacttctggtaaaaaaatatgttctccttaaattccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTTCCCGTGTGGTGCAACAAAGATGACAGTGTCAAGCTCCCCTTCTGCCAAA
             |  |||||  |  | | |  ||| |     | |    | |     ||  |     |    |  | |      ||| |||    |||||||||||||||||||||  ||||||||||| ||||||||    |  || |||||    ||||||||  |  |||||||||| ||||| || | ||| || |
------------gtaagaatttgtacacagtctctgcttcccttcatgcacgcaagctcatgtgaccattttcatttcttaatctcttgaatc---tgcagATAAAAGATGCTTACATGCTCAACTTTTTCGAGAACAACGCAAGTCGTCTTCCTACATGGTGCAATGACAATGACAGTGTGAAGCTTCCTTACTGTCAGA
















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|88902770|gb|CI088308.1|CI088308
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|58687679|gb|CK076366.1|CK076366
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|86504045|gb|CI146678.1|CI146678
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|29642895|gb|CB647902.1|CB647902
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|89185466|gb|CI051794.1|CI051794
EST:     CTGGACTCTTTGACCCCATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|86434558|gb|CI105791.1|CI105791
EST:     CAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAGCAATATGACACGGCTT
genomic: CAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|218493202|gb|FG958053.1|FG958053
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTT
EST: gi|8527546|gb|AU092361.1|AU092361
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCCAACTTTTTTGAGAACAATATGACACGGCT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCT-CAACTTTTTTGAGAACAATATGACACGGCT
EST: gi|58594574|gb|CF992882.1|CF992882
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|29643384|gb|CB648391.1|CB648391
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|29676478|gb|CB672753.1|CB672753
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|87006893|gb|CI275201.1|CI275201
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
EST: gi|29678212|gb|CB674487.1|CB674487
EST:     CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACC                         ATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT
genomic: CTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTT

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: 20 (upstream exon), 31 (downstream exon)
Score: 1

TGGCCAGTCTGCTTCTTGTGTGGCTTACGTCCTTATGATGTACAAGGAGGCTGGACTCTTTGACCCAATTGCCAGCTCTATAGAAGTTACTGAATTCACCgtaagtactc ... ttccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTTCCCGTGTGGTGCAACAAAGATGACAGTGTCAAGCTCCCCTTCTGCCAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcccgcatccaacttctggtaaaaaaatatgttctccttaaattccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTTCCCGTGTGGTGCAACAAAGATGACAGTGTCAAGCTCCCCTTCTGCCAAA
 tattaat  putative branch site (score: 1)
                      taaaaaaatatgttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactaccaaatgatttgaattatgaatatttcctgatcattattaattgcccgcatccaacttctggtaaaaaaatatgttctccttaaattccatgcagATAAAAGATGCTTACAGCCTCAACTTTTTTGAGAACAATATGACACGGCTTCCCGTGTGGTGCAACAAAGATGACAGTGTCAAGCTCCCCTTCTGCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - accaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - gcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa