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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA

Basic information

species Oryza sativa
transcript LOC_Os01g46750.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM5G861300_T01 (Zea mays), 3'ss of exon 15
--------------------------------------------------------------------------tactctcttttactaaact---gtgcctggatgacagtactaatatgatcagctagtt-gcaaagagaggtttgaaaattgaaacatctgttctctgc-ttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
                                                                           | |  | | ||  || |    || ||      | |  |  |  |  ||   ||| || |          | | |||  ||| |||||||     |   ||||||| |||||||||||||||||||||||||||  ||||||||||||||| || ||||||||||| ||||| |||||||| || |||||||| ||||| |||||
gtagtgtgttgcccgttctactgctctgtttttacatagtgatcactattcatgacacacattgttagtagttaaaattccatgtagaaatccagggttccaatcatataccatgaccaaaatttcctattttgtgctcccgcctataaaacctgacacatctgcctcatctgttgcagGTGACATTGGTGAGTGGCAACCTGATGGATCTATGAAAATCATAGACCGTAAAAAGAATATATTCAAACTTTCACAGGGTGAATATGTGGCAGTTGAAAA

upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
tactctcttttactaaactgtgcctggatgaca-gtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
     || |||   |   | ||  || || | |  | ||  || |         |||||     |  ||| |    ||||     || ||| |     |||| || ||||| ||||||| |||  ||||||  |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||||
---gttcatttttcagtttatgtttgaataagatatgcttctacg-----tggattgcatgatcatattttattcatgaa-----tggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA

upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA01G43470.2 (Glycine max), 3'ss of exon 15
--tactctcttt-tactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
  || |   ||| |  |   |        | |     | || |||| | | | | | |      | |  |||     |    |||  || | | |     |||| || ||||| |||||||||||| ||||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||||
gttatttcatttatgttttccaaaattgaggtttatattcttatattagctgttgggttgggtcacaattttccttttattcacaaatgatatat-tcaacagGGGATATTGGAGAGTGGCAACCTAATGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 15
-tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattga-aacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
 |  | || ||||            | || |    || |  ||| || |||| ||||     | || |||     ||   ||||  || | | |     |||| || ||||| |||||||||||| | ||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||||
gttatttcatttatgttttccaaatttgaggtttatattcttat-attagct-gttg-ggtcacagttttcctttttattaacaaatgatatat-tcaacagGGGATATTGGAGAGTGGCAACCTAACGGAAGCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTCGAAAA

upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
-tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctg--cttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
 || |   || |   ||  |||       |      | || |  | |    ||||  |   |||   |||  |  |   |   |||| |   |   ||  |||| ||  |||||||||||||||| |||||||| ||||| || || ||  | || ||||||||||| || || ||||||||||| ||||| || || || ||
gtatttctttctctgaacttgtatacaattagttagaatattg-gtttttgtagtc-cggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA

upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 3'ss of exon 15
--tactctcttttactaaactgtgcctggatgacagtacta-atatgatcagctagttgcaaagagaggtttgaa--aattgaaacatctgttctctgcttgc-agGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
  ||||        | | ||| ||      |  |  | ||| ||||       ||  |   |       |||     | || |   | || |      ||| | ||| ||  ||||||||||||||||  ||||||| ||||| || || || || |||||||| |||||||| ||  | |||||||| ||||| || || || ||
gttactaaaaacctcaacactttgatcattttgctttcctatatatagcattttaaatatcagttcttatttaccttatttaatttaactatgtgtatcttaccagGTGATGTTGGTGAGTGGCAACCAAATGGAAGCATGAAGATAATTGACCGGAAAAAGAACATCTTCAAACTCGCGCAAGGAGAGTATGTCGCTGTTGAGAA

upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
tactctcttttacta--aactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaac-atctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
   |  ||  || |   |  | | | || || | |||  | |  |  ||   |   || |        ||| | ||        ||   || |||  |  |||| ||  |||||||||||||||||||||| || |||||||| || || ||||| ||||| || ||||||||||||||||||||||| || || || || ||
-gtttgctcatattggcatttcttcttgaatta-agttttgaggtcctctattttgtggattcgtttctttaacaaccttgctgatgacttatcttttcacagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA

upper sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttg-cagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
 |    || ||  | || | ||     | ||   | |   | ||    | |   |  |   |  | |   | |    |    | |||  | ||  |  |||| || ||||| |||||||||   |||||   | |||| || || |||||||| ||||| |||||||||||||| ||||||||||| || ||||| |||||
caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaata-agtcaatgatgacatagacaagttctttgtgatgtgtgtatcagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA

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|87031853|gb|CI272554.1|CI272554
EST:     ATGGTTCCATACTG                         GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
genomic: ATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST: gi|58679458|gb|CK068145.1|CK068145
EST:     GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTG                         GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
genomic: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST: gi|87020943|gb|CI269660.1|CI269660
EST:     GATGGATGGTTCCATACTG                         GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCT
genomic: GATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST: gi|27576205|gb|CA998899.1|CA998899
EST:     GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTG                         GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
genomic: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST: gi|29618099|gb|CB623111.1|CB623111
EST:     GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTG                         GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
genomic: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCA
EST: gi|56157720|gb|C25972.2|C25972
EST:     GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTG                         GAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAA-TCATAGAT
genomic: GCGTGAAGACCTTACAAAGGATGTTTTGATTGATGGATGGTTCCATACTGgtatgtcttg ... ctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA
                                     tctgttctctgctt  CT-rich tract
                     tttgaaaattgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactctcttttactaaactgtgcctggatgacagtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - -gtgcctg
- - - - - - - - - - - - - - - - - - - - - - - - - -agttgca