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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccagccgccgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC

Basic information

species Oryza sativa
transcript LOC_Os05g38520.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38520.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009936_T01 (Zea mays), 3'ss of exon 1
gtaag---ccagccgc-cgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
| |||   |||  | | ||||||| ||  | ||| | | |||||||||||| ||| | |||||| | |          | ||    | |   |||||         |  |||||||  |  |  ||  ||||||||| ||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||| |  |||
gcaagtccccattcccgcgccgccgccgtcgccgtcgctgatctgaaaccc-agcgtatctcctgctt-------atcctcggttgtttgtccccgc---------gcacagGAAAGTGTTCGTCCTCATGGCGCCGCCGCAGCCGAAGTCGGGCCTCTTCGTGGGCATCAACAAGGGCCATGTCGTCACCAAGCGCGAGCTGCCTCTGCGC

upper sequence: LOC_Os05g38520.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009936_T03 (Zea mays), 3'ss of exon 1
-----gtaag---ccagccgc-cgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
     | |||   |||  | | ||||||| ||  | ||| | | |||||||||||| ||| | |||||| | |          | ||    | |   |||||         |  |||||||  |  |  ||  ||||||||| ||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||| |  |||
gtaaggcaagtccccattcccgcgccgccgccgtcgccgtcgctgatctgaaaccc-agcgtatctcctgctt-------atcctcggttgtttgtccccgc---------gcacagGAAAGTGTTCGTCCTCATGGCGCCGCCGCAGCCGAAGTCGGGCCTCTTCGTGGGCATCAACAAGGGCCATGTCGTCACCAAGCGCGAGCTGCCTCTGCGC

upper sequence: LOC_Os05g38520.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G850966_T01 (Zea mays), 3'ss of exon 1
-----gtaagccagccgc-cgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
     ||||||||||| | ||||||| || || ||||| | ||||||||||| ||   ||||||||  |        || | | |    ||     |  || |||  ||  |||||||  |  |   |  ||||||||| ||||||| ||||| || || ||||| |||||||||||||| || ||||||||||||||||||||||| || |||
gtaaggtaagccagccccgcgccgccgccgccgccgccgc-gatctgaaacc-tactttctctccttgcgta----tgccctcat---cctcgcttctttgtttgg-cgcacagGAAAGGGTTCGTACTCATGGCGCCGCCGCAGCCAAAGTCGGGCCTTTTCGTTGGCATCAACAAGGGTCATGTCGTCACCAAGCGCGAGCTGCCTCCCCGC

upper sequence: LOC_Os05g38520.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G850966_T03 (Zea mays), 3'ss of exon 1
gtaagccagccgc-cgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
||||||||||| | ||||||| || || ||||| | ||||||||||| ||   ||||||||  |        || | | |    ||     |  || |||  ||  |||||||  |  |   |  ||||||||| ||||||| ||||| || || ||||| |||||||||||||| || ||||||||||||||||||||||| || |||
gtaagccagccccgcgccgccgccgccgccgccgc-gatctgaaacc-tactttctctccttgcgta----tgccctcat---cctcgcttctttgtttgg-cgcacagGAAAGGGTTCGTACTCATGGCGCCGCCGCAGCCAAAGTCGGGCCTTTTCGTTGGCATCAACAAGGGTCATGTCGTCACCAAGCGCGAGCTGCCTCCCCGC

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|55432235|gb|CV729137.1|CV729137
EST:     CCTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CCTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|11610314|gb|AU165990.1|AU165990
EST:     TTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: TTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|286784|gb|D15591.1|D15591
EST:     ATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: ATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88434599|gb|CI690875.1|CI690875
EST:     TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88305586|gb|CI631953.1|CI631953
EST:     GCCGCCGCTTCATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCNGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88422114|gb|CI688909.1|CI688909
EST:     GCCGCCGCTTCATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88719521|gb|CI743031.1|CI743031
EST:     GCCGCCGCTTCATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|33654987|gb|CF277601.1|CF277601
EST:     CCCTAGCCGCCGCCGCTTCATTTCTCCC-----AG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CCCTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88728828|gb|CI752338.1|CI752338
EST:     GCCGCCGCTTCATTTCTCCC-----AG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88724915|gb|CI748174.1|CI748174
EST:     TAGCCGCCGCCGCTTCATTTCTCCC-----AG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: TAGCCGCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|3760010|gb|C97268.1|C97268
EST:     AGCCGCCGCCGCTTCATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: AGCCGCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|11442728|gb|BF430631.1|BF430631
EST:     GCTTCATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|58670481|gb|CK059167.1|CK059167
EST:     CTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|88730456|gb|CI754069.1|CI754069
EST:     CGCCGCCGCTTCATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: CGCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
EST: gi|38481097|gb|CF965186.1|CF965186
EST:     GCCGCTTCATTTCTCCCAGGTAAG                         GAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT
genomic: GCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGT

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: 30 (upstream exon), 75 (downstream exon)
Score: 95

CTCCCTAGCCGCCGCCGCTTCATTTCTCCCAGGTAAGgtaagccagc ... gttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC
                 cgctcac  putative branch site (score: 95)
                                          cttgttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccagccgccgccgccaccacctccgcctccgatctgaaaccctagcctctctcctccctcggcgccgctcacgtagatcttctcccgctgcttgttcgtgcagGAAAAAGGGCTCCCCGATGGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC