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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggatgttcttttcttaagttgaacttatgggatctgaacaattttgcttgatgcaaatttaagttctgagatatgcaaaccatgtgctgctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGTCAATGAGGGACACCCTGACAAGCTCTGCGACCAGATATCCGATGCGGTG

Basic information

species Oryza sativa
transcript LOC_Os01g18860.1
intron # 1
splice site 3'
intron type U2

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|29613152|gb|CB618165.1|CB618165
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|88306969|gb|CI639395.1|CI639395
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|29613180|gb|CB618193.1|CB618193
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|88307055|gb|CI639491.1|CI639491
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|88302179|gb|CI668025.1|CI668025
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|218496320|gb|FG960374.1|FG960374
EST:     CCGCGCCGCCGCGGCCG--GC-ACCCGCGCGCGCGGACTCCTGCCTCTC-                         -TCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|29613182|gb|CB618195.1|CB618195
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|29613115|gb|CB618128.1|CB618128
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|88332873|gb|CI639721.1|CI639721
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|88335828|gb|CI644047.1|CI644047
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|88851448|gb|CI670888.1|CI670888
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|29613220|gb|CB618233.1|CB618233
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|58656797|gb|CK045477.1|CK045477
EST:     CGCGCCGCCGCGGCCAGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CGCGCCGCCGCGGCC-GCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|29613112|gb|CB618125.1|CB618125
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|58609001|gb|CK037034.1|CK037034
EST:     CCGCGCCGGCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|88329719|gb|CI650188.1|CI650188
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
EST: gi|218504347|gb|FG950810.1|FG950810
EST:     CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCG                         GTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT
genomic: CCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGT

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: 66 (upstream exon), 10 (downstream exon)
Score: 1

GGATCTCTCCTCACTCCTCCGCCACCTCAAAGCTCTCCGTTCAAACCGTCCCGCGCCGCCGCGGCCGCTGCAACCCGCGCGCGCGGACTCCTGCCTCTCGgtttgttcct ... ctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGTCAATGAGGGACACCCTGACAAGCTCTGCGACCAGATATCCGATGCGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttgatgcaaatttaagttctgagatatgcaaaccatgtgctgctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGTCAATGAGGGACACCCTGACAAGCTCTGCGACCAGATATCCGATGCGGTG
 gcttgat  putative branch site (score: 1)
                                          ctgcttt  putative PPT
          aaatttaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggatgttcttttcttaagttgaacttatgggatctgaacaattttgcttgatgcaaatttaagttctgagatatgcaaaccatgtgctgctttgtgcagGTCGAAGGAGATGGCTGAGGTTGACACCTTCCTCTTCACTTCCGAGTCCGTCAATGAGGGACACCCTGACAAGCTCTGCGACCAGATATCCGATGCGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT