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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG

Basic information

species Oryza sativa
transcript LOC_Os03g09250.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 4
-tagttccag--tctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
 | |||   |  |||  ||||| ||| ||| | ||||||| |  ||| ||   || | |  |  | |  |  ||  |||   | | | |    | | ||| |||||||| ||||| |||| ||||||||||||||| || ||| |||||||||||||||||||||||||||||||||| |||| ||| ||||| |||||||||
atggtttggggatctagattaacatgattgaagcaacatggctcactggta--tacgtaatccatta-tagaagctatggcttatatgtagccaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGGTAGTTGTGCTGTGGACTGCAAACACTGAAAGGTACAGCAATGTATGTGCTGGTCTCAACGACACAATG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 4
---tagttccag--tctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
   | |||  |   |||  |||||  |||||| |  || |||    ||| ||   || | |  |  | | ||  ||  |||    || | |   || | ||| |||||||| ||||| |||| ||||||||||||| | || ||||||||||||||||||||||||||||| |||||||| || | ||| ||||| ||||| |||
acatggtttgaagatctagattaacgtggttgaagaaatatggttcactagta--taagtaatccatta-cagaagctatggc--ttatgtagctaatgaaacagGGAGTTTAAGGAGAAGAACAAAGTGGACAAGATAGTTGTGTTGTGGACTGCAAACACTGAAAGGTATAGCAATGTGTGCGCTGGTCTCAACGACACGATG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G02210.2 (Glycine max), 3'ss of exon 4
tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
         | ||   ||      |    | | ||| ||| || |      ||  ||| | |  |  |||  || | | |   | ||   |   |   |||| ||| ||||||   | |||||||||||||||||| ||  |||||||||| ||||| || ||||| |||||| |   ||| || || |||||||| |||
------gtatatgtcctatttcaatctacata-cat-acatacatacatacatacatgatctgtatcttattcaggttctaactgttgacatgaactcagGGCGTTTAAGGAAGCCACCAAAGTGGACAAGGTGGTTGTCCTGTGGACTGCCAACACAGAGAGGTATAGCAATTTGGTTGTAGGCCTTAATGACACCATG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------------------------------tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaa-acattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
                                                                                | || |  |||||  ||| ||      ||     |       |  |||   | | |  |  || ||| |    || ||     |||||  | | || |||||||||||| || || | ||||||||| || ||||||||  ||||||| |||||||| ||||| |||||||||||    ||||| || || ||||| | |
gtaacacaacgtctttactattgtaataaaatattctaaggtaacataacggtttatgtttattagcaaattaaatgtaaattttctctctgctataaaatttccaaaattcattagatgtatcatgatcgtaatttttacaagacaatttg-ataatgaaaattttaaaaat-aattagGGAGTTCAAAGAGAAAAACAAAGTGGATAAAGTGGTGGTACTGTGGACGGCAAACACAGAAAGATACAGCAATGTGGTGGTTGGTCTTAACGACACGACG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 3'ss of exon 3
tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgat-attttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
                                  || | |  |||         |||    ||   | |     |  | || | ||| | || ||   ||||||||| ||||| |||| ||||||||| ||| |||| ||||| |||||||||||||| ||  | || ||||||||   ||| || || || || || | |
--------------------------------gtat-atagtcttacatagcaaaattagttagttagttagtgtattgatgtgtttgaatattt--ttagGGAGTTTAAGGAGAAGAACAAAGTGGATAAGTTGGTTGTGTTATGGACTGCAAACACAGAGCGTTATAGCAATGTGATTGTAGGACTTAACGATACGACG

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 4
tagttccagtctgcattaagatggttggaacaacat-gacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
                     |  || |   ||  | ||   | || |  || |     || |   | ||   |||| | |   ||| ||  |||    ||  | ||||||  | | | |||||||||||| || ||||| ||||||||||||||||| ||| | |||||| ||||   ||| || || |||||||| | |
--------------------gtacttcgtcgaatctcgattgagttcttcctct-----cttt---cttttctcatgttttcgctttcatccctt--gcagACACTTCAAGTCACAAACCAAAGTGGACAAAGTCGTGGTTTTGTGGACTGCAAACACGGAACGCTACAGCGATGTGATTGTGGGCCTGAATGACACGAAG

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|29646112|gb|CB651119.1|CB651119
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGANCA-GGTGGTGGTGTTGTGGACTG
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGA-CAAGGTGGTGGTGTTGTGGACTG
EST: gi|58598823|gb|CK009351.1|CK009351
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|3760166|gb|C97424.1|C97424
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|59930133|gb|AB178675.1|AB178675
EST:     TCAYGGGCACCAAGACGGAGCAGATGGAGCAGATCATACA-GGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: TCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCAT-CAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|13420717|gb|AU174807.1|AU174807
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|58675021|gb|CK063708.1|CK063708
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|58598555|gb|CK009083.1|CK009083
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|218487632|gb|FG964358.1|FG964358
EST:     CCAAGAAGGA-CAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAATGTGGTGGTGTTGTGGACTGC
genomic: CCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|29616445|gb|CB621457.1|CB621457
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG
                                  ttttttttattactt  CT-rich tract
                taaacattagacatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttccagtctgcattaagatggttggaacaacatgacaaacttgtgactatgaatgctgtaaacattagacatgatattttttttattacttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG

- - - - -tctgcat
- - - - - - - - - - atggttg
- - - - - - - - - - - - - -gaacaac
- - - - - - - - - - - - - - - - - - -acaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - tgaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgat