Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatcccttaactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC

Basic information

species Oryza sativa
transcript LOC_Os05g03820.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 2
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaatt----ttagtttatccct-taactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
                                                                         | |     |  |    |  |  |   |   |  |     ||| ||||||    |    | ||||||||  |  |||      |  || || || || ||||||| |||||||| |||||||||||||| || || |||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| ||||
------------------------------------------------------------------------ttgagatgctacagccaaacacaagttatgcagttttttttttcttctgatggctggcttcagtttatctttgcaaccttacttgtttctacggatgtagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACATTACATCAAACTTGTGCTGAGGTCAATTCGCATC

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 2
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatccct-taactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
                                                               |  | ||||  |     | | ||| ||     |  ||      | |  | | | |||     | | ||||||||  | ||||      |  || ||||| || ||||||| |||||||| |||||||||||||| || || |||||||||||||| |||||||| ||||| |||||||||||||||||||||||||| |||||||
-------------------------------------------------------------ctttaaatgccaca-----tccaaatagaaggttatgcagttttttaat-gatggctctagtt-tctcagtttatctttgtaacctgaattgtttgtatggatgtagGGAAAGCAAAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACGTTACATCAAACTTGTGCTGAGGTCAACTCACATC

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 3
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatcccttaactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
                                                                             |||  || |       |  ||||| |       | | | ||||  || ||| | || ||   ||||    |     |||| ||    ||||| || || ||||| ||| | || ||||| |||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || ||||| || |
----------------------------------------------------------------------------gtaagcctgacatttgcatcaacaacatgtc--taatattttcttccagttt-aattcatttgttaaaattgcaacgttatgtgaac-cagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACC

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G02570.1 (Glycine max), 3'ss of exon 1
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatcccttaactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
                                                                    | |   || |  |  | |        | |    |||  ||| |     |||    ||    | | |  |  |||    | |  |   ||     ||||||| || ||||| || ||| |||||||||| ||||| ||||| |||||||||   ||| |  ||||||| ||||||||||||| |||| | ||||||||||
----------------------------------------------------------------attgtacttgaaattttatttacaacagttctatttgaaatctgagaccaatttcaattaaacggaatgtgacattta---tatgtaaaaaattctactgcagGGCAAGCAAAGTATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATC

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 3
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaa-tgacagtttgttctgacaattttagtttatcccttaactcaggctacttatatg-gttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
                                                                               |  ||||       |  ||||| |    | | | ||| |||        || ||| |      |  |   | |     |||| |   ||||| || || ||||| ||| | || ||||| |||||||||||||||||||| |||||||||||||| || ||||| ||||||||||| || ||||  || |
-----------------------------------------------------------------------------gtaggctaacatttgcatcaacaagatgtctaatattttcttccagattcatttgttaaaattgcatgttttgttgtcattatgtgaaccagGGGAAGCAGAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACC

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G42900.1 (Glycine max), 3'ss of exon 2
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatcccttaactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
                                                             |    |||       ||| ||  ||  |     | |    ||| |||| |     |||    ||    | | |  |  |||    | |  |   ||     | ||||| || |||||||| ||| |||||||||| ||||| ||||| |||||||||   ||| |  ||||||| ||||||||||||| |||| | ||||||||||
-------------------------------------------------------------ttcttacttgaaactttatttgcaacagtt---ctatttgaaatatgaaaccaatttcaattaaacggaatgtgacgttta---tatgtaaaaaattctactacagGGCAAGCAAAGCATATCATTAGAACCTGGTGGTCAATTTGAGCTTAGTGGTATGCCTTTGAAAACATTGCATCAAACTTGTGATGAGATTAATTCACATC

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 3
-gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatccct-taactcaggctacttatatggttgc-agGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
  ||  ||||| ||||  ||     | |||| |     |   | |  || |    ||     |      ||      | |  |  ||   |   |     | |  | | |   ||   |||     ||||  ||  |     ||||||   ||     | || |  | ||||||| |||||||||||||| |||||||| |||||||| || ||||||||||| |||||||| || || ||||||||||||||||| |||||||||||||
gttaacattctcctgtgtttcatcttttgagccgtttattatttatatacattttcagcctgtagaacatgttagcttcatatacaacacaatgatcggtatatta-taaggtttcagtcttttttttttttttgctgtagataactcgttctgtccttttgttgaccagGGAAAGCAAAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATC

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 3
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatcccttaactcaggctacttat-atggttg--cagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
                                                                  |    |  |   | |  ||    || | |   ||| ||  ||     || |||    | | || || | |  ||    | |     ||||| || ||||  ||||| || |||||||| ||||| ||||| || ||||||||||| ||||| ||||| ||||||||||| || |||||||| ||||||||||| |||||||| |
----------------------------------------------------------------ttatcttcaaaggcactcatagctaaggagcttccaagaag-tg-----tttttcgtttattgttggtatgtttctgttgtgaaatgtcttattattgttgggcagGGGAAGCAAAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACC

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S479_14V6.1 (Physcomitrella patens), 3'ss of exon 2
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaat-tctaatggagaaacaaacaaaaaaatgacagtttgttct-gacaattttagtttatcccttaactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
   ||   || |    |  |||      |     | || ||   |||  | |   |   |   |   | || |||||||   | |  |           ||    |  || ||       | || |    | |   ||   | |  ||   ||  | ||||  ||  |||     |||||  | ||  | ||||| ||||| ||||||||| | ||||| || ||||| || ||| | |||||||| || || ||||||||||||||||
---gtgagctcc--gcaactccttggcaacgtttcatttca--gcttgtagcggtatcaaccat--tccgcagtaattagggtttggttagagtttctgcatttgagagagagcgaaccgtagagagcgatcgaggattt-tgatttcgttctggtgatat--ttatagGATGGTCAAAGTGTATCTTTGGAACCCGGCGGCCAGTTTGAATTGAGTGGAGCGCCTCTGGAGACACTTCATCAAACATGCGCCGAGGTCAATTCACATC

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|33796283|gb|CF324008.1|CF324008
EST:     TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAG                         GGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT
genomic: TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAGgtagtattct ... atggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT
EST: gi|88347509|gb|CI637449.1|CI637449
EST:     TTGATTGGGACAAGATAGTTGAAGAAAATAATGTTATCGGTCTCAAGCAG                         GGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGT
genomic: TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAGgtagtattct ... atggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT
EST: gi|58689197|gb|CK077884.1|CK077884
EST:     TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAG                         GGAAAACAAAGCATTTC
genomic: TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAGgtagtattct ... atggttgcagGGAAAACAAAGCATTTC
EST: gi|88573359|gb|CI664930.1|CI664930
EST:     TTGATTGGGACAAGATAGTTGAAGAAAATAATGTTATCGGTCTCAAGCAG                         GGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGT
genomic: TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAGgtagtattct ... atggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     TTGATTGGGACAAGATAGTTGAAGAAAATAATGTTATCGGTCTCAAGCAG                         GGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGT
genomic: TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAGgtagtattct ... atggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT
EST: gi|88342557|gb|CI637133.1|CI637133
EST:     TTGATTGGGACAAGATAGTTGAAGAAAATAATGTTATCGGTCTCAAGCAG                         GGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGT
genomic: TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAGgtagtattct ... atggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     TTGATTGGGACAAGATAGTTGAAGAAAATAATGTTATCGGTCTCAAGCAG                         GGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGT
genomic: TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAGgtagtattct ... atggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT
EST: gi|88336064|gb|CI647258.1|CI647258
EST:     TTGATTGGGACAAGATAGTTGAAGAAAATAATGTTATCGGTCTCAAGCAG                         GGAAAGCAAAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGT
genomic: TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAGgtagtattct ... atggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT
EST: gi|29677970|gb|CB674245.1|CB674245
EST:     TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAG                         GGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT
genomic: TTGATTGGGACAAGATAGTTGAAGAAAATAACGTTATCGGTCTCAAGCAGgtagtattct ... atggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttctgacaattttagtttatcccttaactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC
         acaattttagtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtattcttctgttatttccgctatgagaccaccttacatgacttagaccaacaattaatgtggactgccgtaattaattctaatggagaaacaaacaaaaaaatgacagtttgttctgacaattttagtttatcccttaactcaggctacttatatggttgcagGGAAAACAAAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC