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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCACGTGCTTGTGGGTGGGCTTTTGGGATGAACATGTTTGACCTGAAAGAGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaaataggtttatcctaccatgcattttctgtctatgaaggtcatgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os10g21890.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g21890.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G028501_T01 (Zea mays), 5'ss of exon 7
TCCACGTGCTTGTGGGTGGGCTTTTGGGATGAACATGTTTGACCTGAAAGAGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaaataggtttatcctaccatgcattttctgtctatgaaggtcatgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgtttgcag
|||||  ||||||||||||||||| ||||||||||||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||||||| ||||||||| ||||| |||||| |         | | |||  ||||      |   | || || | |||  | |     | ||      |  ||   ||       ||  ||    | || |||  |                                
TCCACACGCTTGTGGGTGGGCTTTCGGGATGAACATGTTTGACCTGAAGGAGTGGAAGAAGCGAAATATCACTGGAATATACCATTATTGGCAAGATTTGgtaagtagtggaatgagaaatgt-----actgctgattgcattgcctcgttgcatatagcccatcatttagtgaacctgta-atgaattttgttgtttcgcttactaatagaagacctattgcag--------------------------------

upper sequence: LOC_Os10g21890.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA05G09200.1 (Glycine max), 5'ss of exon 4
TCCACGTGCTTGTGGGTGGGCTTTTGGGATGAACATGTTTGACCTGAAAGAGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaaataggtttatcctaccatgcattttctgtctatgaaggtcatgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgtttgcag
|||    || ||||| ||||| ||||| ||||| ||||||||| |||| ||||||||||| | ||| |||||||| || || |||   ||||||||| |||||| |  |  |  ||       |   | |  ||  || ||| ||| |   |  | |||  ||   |   ||  |||   ||  |  | ||| |||||      |||   ||                                             
TCCTGAGGCGTGTGGCTGGGCATTTGGCATGAATATGTTTGACTTGAAGGAGTGGAAGAAACGAAACATCACTGGTATCTATCATCGGTGGCAAGATATGgtaaat--ttcactga-------tcttattccttctttttatagtttatccatatatata-tatagta-gttgcctgaagattgattttatgaaatta-gttgcctgaagat---------------------------------------------

upper sequence: LOC_Os10g21890.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT4G38270.2 (Arabidopsis thaliana), 5'ss of exon 8
TCCACGTGCTTGTGGGTGGGCTTTTGGGATGAACATGTTTGACCTGAAAGAGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaa--ataggtttatcctaccatgcattttctgtctatgaaggtcatgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgtttgcag
  |  |||||||||||||||| ||||||||||| |||||||||||||||||||||| ||| |  || || || || ||||| || |||||||||||  |||||||  || | |           || | |   ||   ||||| ||  |  ||   |  ||    | ||  || |    |  ||| ||                                                                       
CGCTGGTGCTTGTGGGTGGGCATTTGGGATGAATATGTTTGACCTGAAAGAGTGGAGGAAACGGAACATTACAGGGATATATCACTATTGGCAAGACTTGgtaaggcattggaaatttctcaaaagaaatacatataaatatttttggatgatgaatggatgtgtcaattaatatatgattgatgcag-----------------------------------------------------------------------

upper sequence: LOC_Os10g21890.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv03s0038g03750.t01 (Vitis vinifera), 5'ss of exon 5
TCCACGTGCTTGTGGGTGGGCTTTTGGGATGAACATGTTTGACCTGAAAGAGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaaataggtttatc-ctaccatgcattttctgtctatgaaggtcatgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgtttgcag
||||  ||||||||| ||||| ||||| ||||||||||||||| |||| ||||||| ||||| ||| || ||||||||||| ||||||||||||||  |||||||           |||    |     |  |   |  |  |   |       |||||| |||     || |        || ||    |   |||| | |   ||  || |                                             
TCCAAATGCTTGTGGTTGGGCATTTGGCATGAACATGTTTGACTTGAAGGAGTGGAGGAAGCGAAACATGACTGGAATATATCATTATTGGCAAGACATGgtaag-----------gaagcatttcttttcctctctcttcctccccgctctcttttatctctattcctcaataagcacacataaaaaata---aatttttatgtctattactc--------------------------------------------

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|89184385|gb|CI046950.1|CI046950
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|88839947|gb|CI079401.1|CI079401
EST:     ATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: ATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|86481041|gb|CI123674.1|CI123674
EST:     TTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGGAAGCTGGGCACACTGCCTCCAGGACTGAT
genomic: TTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGT-GGAAGCTGGGCACACTGCCTCCAGGACTGAT
EST: gi|29622298|gb|CB627309.1|CB627309
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29625260|gb|CB630271.1|CB630271
EST:     AGTGGAAGAAGCAAAATATCCCTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29629402|gb|CB634411.1|CB634411
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29622321|gb|CB627332.1|CB627332
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29629341|gb|CB634352.1|CB634352
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|86479242|gb|CI121875.1|CI121875
EST:     AGTGGAAGAAGCGAAATATCACTGGGATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|86501675|gb|CI144308.1|CI144308
EST:     AGTGGAAGAAGCTAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|29628619|gb|CB633630.1|CB633630
EST:     AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT
EST: gi|88966673|gb|CI365896.1|CI365896
EST:     AGCGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTG                         AATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCACGACTGATT
genomic: AGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatg ... ctgtttgcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCACGTGCTTGTGGGTGGGCTTTTGGGATGAACATGTTTGACCTGAAAGAGTGGAAGAAGCAAAATATCACTGGAATATACCATTATTGGCAAGATCTGgtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaaataggtttatcctaccatgcattttctgtctatgaaggtcatgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA