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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAACTCTTGTTGAAGGATCTTCGATGGAACTCTATTGGGAGAATCTCAAGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgattatgtttgttacagacttcctgaacatttattttgtctaattaagtattccgtcatacaagcttttgaagtgaggatatgcagtttctgttttttcctttctgaagctattgagcagacagatttatttatattctgttacag

Basic information

species Oryza sativa
transcript LOC_Os10g37210.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37210.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G032222_T03 (Zea mays), 5'ss of exon 12
CAAAACTCTTGTTGAAGGATCTTCGATGGAACTCTATTGGGAGAATCTCAAGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgattatgtttgttacagacttcct-gaaca---tttattttg---tctaattaagtattccgtcatacaagcttttgaagtgaggatatgcagtttctgttttttcctttctgaagctattgagcagacag---atttatttatattctgttacag
|||  | || ||||||||||||||||||||||| || |||||||| |||||||||||||||||||||||||| ||| ||| |||| ||||||| ||||||||||||| |||| ||| |    || ||  |  ||||   ||   ||||   |||  |||| |||   ||  |  |||||      |  | || | |||  | | | || |   ||||||||  || | ||  ||  |   |||||||  | || | || |||
CAAGTCCCTCGTTGAAGGATCTTCGATGGAACTGTACTGGGAGAACCTCAAGAAGTCATGGATATGGGAAGAACTTCATAAAGCTAGGAATTATAGACCAgtatgtggttat-tttatggttgattttttcaaacaaacttagctttggtatctggttaaatatctagttctgtaagctgacaggggaaaga-aggcaaatcc-gcttatctttttctgaacatactaagttgaatgtgtatttattacttttttcttccag

upper sequence: LOC_Os10g37210.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv05s0102g01110.t01 (Vitis vinifera), 5'ss of exon 12
CAAAACTCTTGTTGAAGGATCTTCGATGGAACTCTATTGGGAGAATCTCAAGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgattatgtttgttacagacttcctgaacatttattttgtctaattaagtattccgtcatacaagcttttgaagtgaggatatgcagtttctgttttttcctttctgaagctattgagcagacagatttatttatattctgttacag
  |    |||  |||||| ||    ||||||   ||||||||   ||| | ||| ||||||||||||||||| ||| ||| ||||||||||||| | || ||  ||||     ||   |  |  ||          ||| |    ||   | | |     ||  |  |  ||      |      | | ||  |||| ||                                                    
TGATGTACTTCATGAAGGCTCGAGCATGGAAAAATATTGGGATGGTCTAAGGAATTCATGGATATGGGAAGAACTTCATAAAGCTCGGAATTACCGTCCGgttagtgagacaattaagtgtattctcttaactttcttaatcatcctttctcacttagtggtagtgtatactacaagggctgccttgtacatattctatt----------------------------------------------------
















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|218502645|gb|FG955089.1|FG955089
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATCTGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|29615151|gb|CB620164.1|CB620164
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|218483729|gb|FG951541.1|FG951541
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTG
EST: gi|29657656|gb|CB653931.1|CB653931
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|29675569|gb|CB671844.1|CB671844
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|29662394|gb|CB658669.1|CB658669
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGTTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTTTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|218486085|gb|FG956984.1|FG956984
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|29637767|gb|CB642776.1|CB642776
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|86859459|gb|CI278866.1|CI278866
EST:     AGAAGTCATGGATATGGCAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCANGGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|29669361|gb|CB665636.1|CB665636
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|29667105|gb|CB663380.1|CB663380
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|29676401|gb|CB672676.1|CB672676
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|29659147|gb|CB655422.1|CB655422
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
EST: gi|29681493|gb|CB677768.1|CB677768
EST:     AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCA                         GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG
genomic: AGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG

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: 74 (upstream exon), 50 (downstream exon)
Score: 12

CAAAACTCTTGTTGAAGGATCTTCGATGGAACTCTATTGGGAGAATCTCAAGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgatt ... tctgttacagGCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAACTCTTGTTGAAGGATCTTCGATGGAACTCTATTGGGAGAATCTCAAGAAGTCATGGATATGGGAAGAGCTTTATAGAGCTCGGAATTACAGACCAgtatgtgattatgtttgttacagacttcctgaacatttattttgtctaattaagtattccgtcatacaagcttttgaagtgaggatatgcagtttctgttttttcctttctgaagctattgagcagacagatttatttatattctgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT