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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggttattctgattttctgattactagagaatttcacctttttgaacatcttttgaagttaagttcaacgctgaattgcctatgctcttctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTACTAAGCCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g15310.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G095114_T01 (Zea mays), 3'ss of exon 5
atggttattctgattttctgattac-tagagaatttcacctttttgaacatcttttgaagtta--agttcaacgctgaattgcct-atgctcttctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTACTAAGCCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAG
      |||   | | |||| | |  |||||  ||    | |||    |||  | |   ||||  | ||||    | ||||   | |||||    | ||||||||||||| |||||||||||| ||||||||||||||||| || ||  | ||| |||| ||||||||||||||||| || |||||||| |||||||| || ||
---aacattgc-agtatctgttcatgtagagttttgagtcatttgttgcatagtatttggttaccaattcaggattcaatttttttatgctaccatcaatgcagATAGGAAGCCACCAGGTGTTGGCCGCGGAAGAGGAAGGGGGGACGTTGGTGCTAAACCTGGAGGCAGAGGCATCGGACGTGGCCAAGATGATGGAGGTAG

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 5
--atggttattctgattttctgattactagagaatttcacctttttga-acatcttttgaagttaagtt-caacgctgaattgcctatgctcttctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTACTAAGCCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAG
  ||   ||||   |   |||| | | |  ||||||| |    || |   ||| ||     ||||  |    | | | || |   ||| ||    ||||  ||||||||| |||||||||||| ||||| ||||||||||| || ||  | ||| |||| |||||||||||||||||||| |||||||| |||||||| || ||
tgataaatattgc-agcatctgttca-tgtagaatttgagtcattcgttgcatattaattggttacctagtcaggattaactttttatactgccataaa--cagATAGGAAGCCACCAGGTGTTGGCCGTGGAAGAGGAAGGGGGGACGTCGGTGCTAAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG
















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|88848532|gb|CI087054.1|CI087054
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|88214587|gb|CI214436.1|CI214436
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|86504317|gb|CI146950.1|CI146950
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|88202538|gb|CI200893.1|CI200893
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|88979842|gb|CI026148.1|CI026148
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|89199230|gb|CI255496.1|CI255496
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|88208022|gb|CI207871.1|CI207871
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|88241907|gb|CI241756.1|CI241756
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|88214580|gb|CI214429.1|CI214429
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGTTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|3761805|gb|C99053.1|C99053
EST:     TCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGT
genomic: TCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGG-CCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGT
EST: gi|89170615|gb|CI039892.1|CI039892
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|3761804|gb|C99052.1|C99052
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|88241526|gb|CI241375.1|CI241375
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGCGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|87025899|gb|CI282476.1|CI282476
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
EST: gi|89193834|gb|CI018152.1|CI018152
EST:     GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAG                         ATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA
genomic: GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTA

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: 69 (upstream exon), 42 (downstream exon)
Score: 19

GTGATTGACAAGGTCCAGGAAGAGACTTCAAAGAGCAGATCAGgtatgtaccc ... ctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTACTAAGCCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatcttttgaagttaagttcaacgctgaattgcctatgctcttctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTACTAAGCCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAG
                                           ttctaaa  putative branch site (score: 19)
                                      tgctcttct  CT-rich tract
                                           ttctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggttattctgattttctgattactagagaatttcacctttttgaacatcttttgaagttaagttcaacgctgaattgcctatgctcttctaaatgcagATAGGAGGCCACCAGGTGTAGGCCGCGGAAGAGGAAGAGGTGATATAGGTACTAAGCCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - -ttctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctatgc