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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgttcagatcaagatactactaatatgccgtcatgttcttcacccctgtttctggatactgcatgttcttatagtcttgaattgatcttgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAGTCTGCAGATCTTGTAATCAGATCGGTGGATTTGTCAAGATAAGAGTCCA

Basic information

species Oryza sativa
transcript LOC_Os12g40880.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40880.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G035338_T02 (Zea mays), 3'ss of exon 11
---catgttcagatcaagatactactaatatgccgtcatgttcttcacccct--gtttctggatactgcatgttcttatagtcttgaattgatcttgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAGTCTGCAGATCTTGTAATCAGATCGGTGGATTTGTCAAGATAAGAGTCCA
   ||||||||| |   |  | | || ||   | |||||  || |||   ||  ||||||| ||  |||  ||| ||||    |  ||||| |||||||||||||||||| || || ||||| || || |||||||||||| || | ||||  |||  ||| || ||||| |||||||| || || || ||||| ||    || |
aatcatgttcagct---gtcaatgctgatgccctgtcattctcctcaatgctcagtttctgaattttgccagttattat--cttgaaattgttcttgtgaatcagATCTCCTACAACGACCGACCGAATGCAGAGCTTATCCTGGAATCAAGGAAGAATGCTGACCTTGTGATCAGATCAGTAGACTTCTCAAGCTAGTGTTCAA
















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|88555903|gb|CI486193.1|CI486193
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88972880|gb|CI019499.1|CI019499
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|12622959|gb|AU173172.1|AU173172
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88519788|gb|CI447442.1|CI447442
EST:     GAAAAGAGCCAGATGTAGCAGCATGGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAA
genomic: GAAAAGAGCCAGATGTAGCAGCAT-GGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAA
EST: gi|88967316|gb|CI002498.1|CI002498
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88457129|gb|CI531728.1|CI531728
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88484850|gb|CI422121.1|CI422121
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|13895854|gb|AU068162.2|AU068162
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88554268|gb|CI484437.1|CI484437
EST:     GAGAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GA-AAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88530957|gb|CI459391.1|CI459391
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88522664|gb|CI449421.1|CI449421
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88554994|gb|CI485212.1|CI485212
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|89194890|gb|CI003354.1|CI003354
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88524459|gb|CI450372.1|CI450372
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88526128|gb|CI452507.1|CI452507
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
EST: gi|88559654|gb|CI490251.1|CI490251
EST:     GAAAAGAGCCAGATGTAGCAGCATGGCGG                         ATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG
genomic: GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAG

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: 29 (upstream exon), 41 (downstream exon)
Score: 5

GAAAAGAGCCAGATGTAGCAGCATGGCGGgtaattctct ... tgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAGTCTGCAGATCTTGTAATCAGATCGGTGGATTTGTCAAGATAAGAGTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgtttctggatactgcatgttcttatagtcttgaattgatcttgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAGTCTGCAGATCTTGTAATCAGATCGGTGGATTTGTCAAGATAAGAGTCCA
                                    aattgat  putative branch site (score: 5)
                      ttcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgttcagatcaagatactactaatatgccgtcatgttcttcacccctgtttctggatactgcatgttcttatagtcttgaattgatcttgtgaatcagATCTCGTATAATGACCGGCCAAACGCAGAGCTTATCATGAAGTCAAAAAAGTCTGCAGATCTTGTAATCAGATCGGTGGATTTGTCAAGATAAGAGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
catgttc
- - - - - - - - - - - - -tatgccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcttgaa