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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgatttcatttttgctgcgtgacactaaccatgtaatccagttatttcaatggcttaccaatgaccgtgtttgtggtatttcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os12g07060.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07060.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G118316_T01 (Zea mays), 3'ss of exon 15
gtattgatttcatttttgctgcgtgacactaaccatgtaatccagttatttcaatggcttaccaatgaccgtgtttgtggtatttcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
     |  | |||| ||    | |   | |   ||  |  ||  |||   |  ||  ||||    | ||| || |||| |||||   ||  |||||||| |||||||||||||| ||||| ||||| |||||| |||||||||
-----gtatgcattcttcactcttctgaattttcaaat--tcttgttgcat-gatttcttaaaggttaccttgcttgtcgtattatttgtccagGTTCGTCAAGGTACCCAACCTGGAGAGAAGGTCGTCCTCCGGGGCAAAG
















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|218480866|gb|FG958004.1|FG958004
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGAGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|218491432|gb|FG970302.1|FG970302
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|218496597|gb|FG964017.1|FG964017
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|86478861|gb|CI121494.1|CI121494
EST:     ACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: ACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|33806063|gb|CF328911.1|CF328911
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|89175720|gb|CI042741.1|CI042741
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|88845990|gb|CI084720.1|CI084720
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|88228631|gb|CI228111.1|CI228111
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|58680289|gb|CK068976.1|CK068976
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|86501480|gb|CI144113.1|CI144113
EST:     AGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTGCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: AGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGT-CAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|88228692|gb|CI228172.1|CI228172
EST:     CAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: CAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|58657698|gb|CK046378.1|CK046378
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|218487624|gb|FG950213.1|FG950213
EST:     GTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: GTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|86874336|gb|CI335948.1|CI335948
EST:     GTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: GTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
EST: gi|88243593|gb|CI243990.1|CI243990
EST:     TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG                         GTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
genomic: TAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG

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: 65 (upstream exon), 49 (downstream exon)
Score: 25

GCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAGgtattgattt ... tcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccagttatttcaatggcttaccaatgaccgtgtttgtggtatttcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG
                ggcttac  putative branch site (score: 25)
                                         tatttcct  putative PPT
      ttatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgatttcatttttgctgcgtgacactaaccatgtaatccagttatttcaatggcttaccaatgaccgtgtttgtggtatttcctgatcagGTTCGCCAAGGTACCCAACCAGGAGAAAAGGTTGTCCTCAGGGGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG