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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggatcaattaacttcgctccagtattcttttgagtgatgagttgtctcttctcttcaactgattgggaaactttttatcttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGATGTAAAGGGTATAACCATCACTGCTGATGGGACAGGTGCTGTATTTGAT

Basic information

species Oryza sativa
transcript LOC_Os09g34910.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34910.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G164956_T01 (Zea mays), 3'ss of exon 12
gtgagtggatcaattaacttcgctccagtattcttttgagtgatgagttgtctcttctcttc-aactgattgggaaactttttatcttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGATGTAAAGGGTATAACCATCACTGCTGATGGGACAGGTGCTGTATTTGAT
           || | |||  | |    | | ||| ||  | | |||     |||  |||||  | | | ||| || | ||||||   | || || |||| | || |||  ||||||||||| ||||||||||||| |||||||||||||||||||  |||| |||| |||||||| || || | ||||||||||
---------gtaagtgact--ggtaatttgtgcttctggttcacgagggtcatctgatcttctgattaaatggaaatccttttatg--cctgcagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGAGAAACTTGCAGATGTAAAGGGTGCAACCCTCACGGCTGATGGAACGGGGGTTGTATTTGAT

upper sequence: LOC_Os09g34910.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G149520_T01 (Zea mays), 3'ss of exon 8
gtgagtggatcaattaacttcgctccagtattcttttgagtgatgagttgtctcttctcttcaactgattgggaaactttttatcttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGATGTAAAGGGTATAACCATCACTGCTGATGGGACAGGTGCTGTATTTGAT
           || | |||  | |    | | ||| ||  | ||||||  |||          | | | ||| ||  |  || ||| | ||||| |||| | || |||  ||||||||||| ||||||||||| | |||||||||||||||||||   ||| |||| |||||||| ||||| | ||||||||||
---------gtaagtgact--ggtaatttgtgcttctggttcatgagtgttct---------gattaaatggaaa--tccttctctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGATGTAAAGGGTGCCACCCTCACCGCTGATGGAACAGGAGTTGTATTTGAT
















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|29679594|gb|CB675869.1|CB675869
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|218480006|gb|FG954443.1|FG954443
EST:     AACCACACTACATTACTTCTTCTAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAAGAGAGACTTGCAG
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAA-GAGAGACTTGCAG
EST: gi|29622801|gb|CB627812.1|CB627812
EST:     AACCACACTACATTACTTCTTCTAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|29637933|gb|CB642942.1|CB642942
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|88839408|gb|CI005196.1|CI005196
EST:     ATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: ATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|29672112|gb|CB668387.1|CB668387
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTG
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTG
EST: gi|88964243|gb|CI045436.1|CI045436
EST:     GATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: GATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|218486017|gb|FG967018.1|FG967018
EST:     AACCACACTACATTACTTCTTCTAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|29628389|gb|CB633400.1|CB633400
EST:     AACCACACTACATTACTTCTTCTAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|87023726|gb|CI286477.1|CI286477
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTT
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTT
EST: gi|87008347|gb|CI301105.1|CI301105
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|218504157|gb|FG948763.1|FG948763
EST:     AACCACACTACATTACTTCTTCTAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|87035352|gb|CI189974.1|CI189974
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|29636722|gb|CB641731.1|CB641731
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|29687238|gb|CB683513.1|CB683513
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|29662539|gb|CB658814.1|CB658814
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|218487667|gb|FG948994.1|FG948994
EST:     AACCACACTACATTACTTCTTCTAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|218495874|gb|FG947056.1|FG947056
EST:     AACCACACTACATTACTTCTTCTAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|29662538|gb|CB658813.1|CB658813
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTTTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|29672113|gb|CB668388.1|CB668388
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
EST: gi|86482307|gb|CI124940.1|CI124940
EST:     AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG                         ATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA
genomic: AACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGA

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: 71 (upstream exon), 73 (downstream exon)
Score: 106

GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGGgtgagtggat ... cttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGATGTAAAGGGTATAACCATCACTGCTGATGGGACAGGTGCTGTATTTGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgagttgtctcttctcttcaactgattgggaaactttttatcttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGATGTAAAGGGTATAACCATCACTGCTGATGGGACAGGTGCTGTATTTGAT
                       aactgat  putative branch site (score: 106)
                                     ctttttatcttcttgt  putative PPT
                                  aaactttttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtggatcaattaacttcgctccagtattcttttgagtgatgagttgtctcttctcttcaactgattgggaaactttttatcttcttgtagATTTGTTCTTTCTACTTTGAAAAGGTTTATGCCAGAAGAGAGACTTGCAGATGTAAAGGGTATAACCATCACTGCTGATGGGACAGGTGCTGTATTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT