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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttggtgctaaacttagctatcaatgttttggccaactcactaaatttcttgcatatatatcctcttttgcatattgattcagattccttctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGCTGAACTGGAGAGGGAGCAGTACTGGCCGTCTGAGAAGCTGAGGATATCG

Basic information

species Oryza sativa
transcript LOC_Os10g28200.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 1
-ttttggtgctaaacttagctatcaatgttttggccaactcactaaatttcttgcatatatatcct---cttttgcatattgattcagattccttctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGCTGAACTGGAGAGGGAGCAGTACTGGCCGTCTGAGAAGCTGAGGATATCG
  |  | || | | |   |  | |     ||| || ||||    |  | | |   ||  ||   ||   || | ||| |||||||    | | |    ||||||||||||||||   ||||||| ||  || ||||| |||||||||||||| ||||| |||||||||||||  |||||||||  ||||||||||||||| |||
tatacgttgatgatccatg--agctggactttagc-aactgctgatgtgtgtgtgattcatgagctggactctagca-attgattgtcttgcttcaaatgacagAATGGGGAGCAGCGAGAAGACCGTTACCGCTTACGGCGAGTACACCTACGCTGAGCTGGAGAGGGAGCCCTACTGGCCGAGTGAGAAGCTGAGGATTTCG
















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|33664528|gb|CF295495.1|CF295495
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29639582|gb|CB644591.1|CB644591
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29662156|gb|CB658431.1|CB658431
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|33684622|gb|CF312861.1|CF312861
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29612786|gb|CB617799.1|CB617799
EST:     GGCCGCTTCCGATCCCCCTACAAGCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCCATGC
genomic: GGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|33658335|gb|CF280948.1|CF280948
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|33693065|gb|CF321304.1|CF321304
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|88367131|gb|CI563895.1|CI563895
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTGCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29676976|gb|CB673251.1|CB673251
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|33796923|gb|CF324325.1|CF324325
EST:     TCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: TCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29668588|gb|CB664863.1|CB664863
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|14981732|gb|BI306410.1|BI306410
EST:     GCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAATGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29656792|gb|CB653067.1|CB653067
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29663088|gb|CB659363.1|CB659363
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|13420589|gb|AU174679.1|AU174679
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|58677087|gb|CK065774.1|CK065774
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29669312|gb|CB665587.1|CB665587
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|117230143|gb|CT846231.1|CT846231
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAATGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29680859|gb|CB677134.1|CB677134
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|58672465|gb|CK061151.1|CK061151
EST:     GCGGCGG-CGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|33657604|gb|CF280218.1|CF280218
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|8858460|gb|AU095778.1|AU095778
EST:     TTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AANGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: TTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29688060|gb|CB684335.1|CB684335
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
EST: gi|29672449|gb|CB668724.1|CB668724
EST:     GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAG                         AATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC
genomic: GCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGC

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: 46 (upstream exon), 66 (downstream exon)
Score: 17

CTCCTCCTCCCTATCCCCTTCTCCCCCCTCTCTCTCTCTCTCCACCCCGCGCGGCGGCCGCTTCCGATCCCTCTCCGACCGACCAAGCGCCGCCTCCAAGgtatttccct ... tctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGCTGAACTGGAGAGGGAGCAGTACTGGCCGTCTGAGAAGCTGAGGATATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcttgcatatatatcctcttttgcatattgattcagattccttctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGCTGAACTGGAGAGGGAGCAGTACTGGCCGTCTGAGAAGCTGAGGATATCG
                            tattgat  putative branch site (score: 17)
                                        ttccttcttt  putative PPT
         atatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttggtgctaaacttagctatcaatgttttggccaactcactaaatttcttgcatatatatcctcttttgcatattgattcagattccttctttgacagAATGGGGAGCTCGGAGAAGAACGGAACTGCTTATGGCGAGTACACCTATGCTGAACTGGAGAGGGAGCAGTACTGGCCGTCTGAGAAGCTGAGGATATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - ggtgcta
- - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - -cactaaa
- - - - - - - - - - - - - - - - - - - - - - - - tcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattca