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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgactgcctcgattagctaattaaggctggtacggtttggtttcttggtactatgatattcttgctcactgctaacttgaattgtgaaatatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGCAGAAATTCTATAGCACTAGAACAG

Basic information

species Oryza sativa
transcript LOC_Os08g22864.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g22864.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G327394_T01 (Zea mays), 3'ss of exon 22
ctgactgcctcgattagctaattaaggctggtacggtttggtttcttgg--tactatg-atattcttgctcactgctaacttgaattgt--gaaatatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGCAGAAATTCTATAGCACTAGAACAG
  |  ||  |  |||   ||  |   |     |    |||||| |  ||  |||  || | |||      | || || || |   || |  | |   |||| |||||||| ||||| |||||||| || || |||||||| ||||| ||||||||||| ||||| ||||| || ||||||
--gtttgtttttatt--ttagctgcagtcttgagttcttggttgcaaggcctacactgtaaattgagataccctacttacgttttttatttgtatgtttttccagGCACTTGCTCAAATGAAGTCAATAAACTTGTTAGGAGTCCAGCAAATATGCAGGAATTCGATAGCTCTGGAACAG
















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|86437704|gb|CI119624.1|CI119624
EST:     ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
EST: gi|29624113|gb|CB629124.1|CB629124
EST:     ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
EST: gi|58586846|gb|CF985154.1|CF985154
EST:     ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
EST: gi|86480164|gb|CI122797.1|CI122797
EST:     ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
EST: gi|29626007|gb|CB631018.1|CB631018
EST:     ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
EST: gi|86480174|gb|CI122807.1|CI122807
EST:     ATTATGTATTTGTTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
EST: gi|88670678|gb|CI724794.1|CI724794
EST:     ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
EST: gi|88671305|gb|CI724351.1|CI724351
EST:     ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
EST: gi|58692351|gb|CK081038.1|CK081038
EST:     ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
EST: gi|88996514|gb|CI260018.1|CI260018
EST:     ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAG                         GCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC
genomic: ATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGC

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: 71 (upstream exon), 75 (downstream exon)
Score: 24

CGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGGAATTATGTATTTGGTGGGATTTCTAGCGTTGCTGCTAATGCATCGATAAAGgtttgttatg ... tatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGCAGAAATTCTATAGCACTAGAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtactatgatattcttgctcactgctaacttgaattgtgaaatatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGCAGAAATTCTATAGCACTAGAACAG
                         tgctaac  putative branch site (score: 24)
                                             tatttttc  putative PPT
                                   aattgtgaaatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgactgcctcgattagctaattaaggctggtacggtttggtttcttggtactatgatattcttgctcactgctaacttgaattgtgaaatatttttcagGCACTCGCTCAGATGAAGTCGATCAATTTGTTAGGGGTCCAACAAATATGCAGAAATTCTATAGCACTAGAACAG

-tgactgc
- - - - - - - - - - - - -ggctggt
- - - - - - - - - - - - - - - - - - - - - - - tggtact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgaat