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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacttgcttaaatggtacacctaagctatttatactatatgctgtttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os06g13820.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 8
gacttgcttaa--atggtacacctaagctatttatactatatgct-gtttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG
    || | ||   ||||     ||   |   |||    ||||||  |||||   |    | ||   ||   || ||   ||   |  ||   ||  |||||| ||||||||||| || || |||||||||||||| |||||||| ||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| 
tttctgatcaattgtggttgctatatattgaatatggcttatgcttattttttgggtacattttgaatagcttttatattttcaatcatt---tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 20
gacttgcttaaatggt-acacctaagctatttatactatatgctgtttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG
 |  |   | |  | |      |    ||| |  | |||    | | |||| |   | ||   | | |      ||  | |     |  | || ||||||| |||||||||||||| || ||||||||||| || |||||||||||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| 
-atatttctgatcgattgtggttgccatatattcagtatggcttatgtttatttttagtacattttgaatagcttttgtatttcaatcatttctttaccagCGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA
















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|29622848|gb|CB627859.1|CB627859
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|86482222|gb|CI124855.1|CI124855
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCCTGCAAGAGGACCATAATG
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTT-CTGCAAGAGGACCATAATG
EST: gi|29614012|gb|CB619025.1|CB619025
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|29657562|gb|CB653837.1|CB653837
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|218497504|gb|FG955306.1|FG955306
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|25798429|gb|CA754390.1|CA754390
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|86898985|gb|CI296187.1|CI296187
EST:     GAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
EST: gi|87040350|gb|CI194972.1|CI194972
EST:     GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG                         TGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC
genomic: GTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGC

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: 68 (upstream exon), 74 (downstream exon)
Score: 82

GCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAGgttgatgaat ... tcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG
                      tcttaat  putative branch site (score: 82)
                            ttcctttgcttttttt  CT-rich tract
          attattatctaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacttgcttaaatggtacacctaagctatttatactatatgctgtttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG

- - tgcttaa
- - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -tgccatt