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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaaagaaaataatcttcttgcttgatttaagcttaactgttccaactcctattccagtttgctcctggagtttcatattgacatttgagcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAACGTAAGATGATGAAAAACAAACCAATGGATTGAAGCTTCAGTGACACTA

Basic information

species Oryza sativa
transcript LOC_Os01g54910.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G128688_T01 (Zea mays), 3'ss of exon 18
ccaaaagaaaataatcttcttgcttgatttaagcttaactgttccaactcctattccagtttgctcctggagtttcatattgacatttgagcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAACGTAAGATGATGAAAAACAAACCAATGGATTGAAGCTTCAGTGACACTA
       |  |||||| |||| |   |||    || ||          |    |  ||  ||  |  |   |    |||||||||||||||| |||||||||||||||||||||| | || ||||| ||||| ||  ||||| |||| || |||||||||||||||||||| || ||| |||  | || ||| ||||  |
ttttcttattataatcgtcttacaatattgttcctgaagcaactggcatttagtatcaagttatttatattgacatatattgacatttgagcctcatcagGTTACTCCCAAGGTCGTACGTCTTCGAAAGAAGTACTTGGATTCCACTAAGCGTAAGATGATGAAAAACAAGCCTATGAATTAGAACTCCAGAGACAACA
















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|58668676|gb|CK057362.1|CK057362
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|88561572|gb|CI492289.1|CI492289
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|87040973|gb|CI195595.1|CI195595
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|88198384|gb|CI198234.1|CI198234
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|9864965|gb|AU100715.1|AU100715
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|87020890|gb|CI269607.1|CI269607
EST:     TGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|25806199|gb|CA762160.1|CA762160
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTGGGCTTCGGAAGAAATATCTGGATGCCCCGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|218480472|gb|FG958725.1|FG958725
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCT
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCT
EST: gi|88976925|gb|CI257621.1|CI257621
EST:     TGAGTTTGGAAGAGCCCATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|58690249|gb|CK078936.1|CK078936
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|58686388|gb|CK075075.1|CK075075
EST:     TTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|87040029|gb|CI193238.1|CI193238
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|88955134|gb|CI721765.1|CI721765
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|29629970|gb|CB634979.1|CB634979
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|87040844|gb|CI195466.1|CI195466
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
EST: gi|88904755|gb|CI712054.1|CI712054
EST:     TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAG                         GTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA
genomic: TGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAA

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: 51 (upstream exon), 71 (downstream exon)
Score: 27

ATGAGTTTGGAAGAGGCAATTGGATATGTTGCTGCAGATGAGCTTATTGAGgcaagttttc ... gcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAACGTAAGATGATGAAAAACAAACCAATGGATTGAAGCTTCAGTGACACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcctattccagtttgctcctggagtttcatattgacatttgagcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAACGTAAGATGATGAAAAACAAACCAATGGATTGAAGCTTCAGTGACACTA
                                tattgac  putative branch site (score: 27)
                                              cttcatc  putative PPT
                           tttcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaaagaaaataatcttcttgcttgatttaagcttaactgttccaactcctattccagtttgctcctggagtttcatattgacatttgagcttcatcagGTTACTCCCAAGGTCATTCGGCTTCGGAAGAAATATCTGGATGCCACGAAACGTAAGATGATGAAAAACAAACCAATGGATTGAAGCTTCAGTGACACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - -aaaataa
- - - - - - - - - -ttgcttg
- - - - - - - - - - - - - - - - - - - ctgttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatttg