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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacaacgttttgcattttatatcactgctaccctagagcaccatgcgcgtattttgcatttttgctcatcatgactgaaaatttttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGACGCAGTGAACTCCACAGCAGGGATTT

Basic information

species Oryza sativa
transcript LOC_Os03g18310.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 20
gtgagacaacgttttgcattttatat-cactgctaccctagagcaccatgcgcgtattttgcatt---tttgctcatcatgactgaaaattt-ttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGACGCAGTGAACTCCACAGCAGGGATTT
 | | ||||  |||  | |   | |  ||  | |   || |     | ||  |  |  | | |||   | |  |     || || |||||   || || |||||||| || |||||||||||||||||||||||||||||||||||||||||||||||| | |||||||||||||| ||| |  |  ||||||| ||| | |
cttaaacaa-atttgacttaacacaaacatagatgggcttgtatttc-tgatcagaagtagtattgattatttttgctgtggctaaaaatacgttcctgcagATACCTCTACATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAACGGTACAAACTCATGGATGCAATCCATCCCACAGCGGGGTTGT

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 23
------gtgagaca-acgttttgcattttatatcactgctaccctagagcaccatg-cgcgtattttgcatttttgctcatcatgactgaaaatttttg--ctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGAC-GCAGTGAACTCCACAGCAGGGATTT
      ||| |    || || |   ||  | |   || |     | | | |  |||  |  |||  || |  |      ||| | ||   | |||| ||   ||||| | || |||||||| || ||||||||||| ||||| ||  | ||||| |||||||||||||| ||||| |||||| | | |||| |  | |  ||    | 
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgctgaagat------atc-taacatgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTTCT-

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 29
------gtgagaca-acgttttgcattttatatcactgctaccctagagcaccatg-cgcgtattttgcatttttgctcatcatgactgaaaatttttg--ctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGACGCAGTGAACTCCACAGCAGGGATTT
      ||| |    || || |   ||  | |   || |     | | | |  |||  |  ||| ||| |  |      ||| | ||   | |||| ||   ||||| | || |||||||| || ||||||||||| ||||| ||  | ||||| |||||||||||||| ||||| ||||||  |                      
atttttgtggggttcacattgtcagttggagaaatcttcacttttggtgaatgatgatgaatatgttgaagat------atc-taacgtgagatttgtgatttccagGTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGA----------------------

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 22
gtgagacaacgttttgcattttatatcactgctaccctagagcaccatg-cgcgtattttgcatttttgctcatcatg-actgaaaatttttgc---tccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGAC-GCAGTGAACT-CCACAGCAGGGATTT
   | |  |   | ||        | ||    |    |  | |    |   |   || ||| ||||  ||     ||  | ||  | |||   |   | ||||| || || ||||| ||||| || |||||| |||| ||| | |||||  ||||||||||||||||||| |||||| | | ||||   |   || || ||   
--aaaaggaaaatctgtgaggctcaccatccattttgtgaaacgttttaatgtaaatcttgaatttgcgcaagatatctaatgtgagtttgctcatttacagATGCCCCTCCATACGATAATAGAAATACAATTGGGAGTTACAGGTGTCGAAGAGAAAAGATACAAACTAATGGACTGAAATGAATAACTGAAGGAGAGAA--

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 33
gtgagacaacgttttgcattttatatcactgctaccctagagcaccatgcgcgtattttgcatttttgctcatcatgactgaaa-atttttgctc-----cagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGAC-GCAGTGAACTCCACAGCAGGGATTT
   | |  |   | ||   || |   ||    |    |  | |    | |  |||  |      ||||| ||  ||  || |      |||||||     ||||| || || ||||| ||||| ||||||||| |||| ||| |||||||| ||||||||||||||||||| |||||| | | ||||||  |  | | | ||  
caaaaaggaaaatctgaggttcac--catccattttgtgaaacgttttac-tgtaaatcatgaatttgcgcaagatatctaatgtgagtttgctcatttacagATGCCCCTCCATACGATAATAGAGATACAATTGGGAGTTACTGGTGTTGAAGAGAAAAGATACAAACTAATGGACTGAAATGAACTGAAGGGAAAGAATA-

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 24
-----gtgagacaacgttttgcattttatatcactgctaccctagagcaccatgcgcgtattttgcatttttgctcatcatgactgaaaatttttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGAC-GCAGTGAACTCCACAGCAGGGATTT
     ||| |        |  || ||      |     ||  | ||  |        | || |        |    | | |||    |  | |    ||||| | || |||||||| || ||||||||||| ||||| ||  | ||||| |||||||||||||| ||||| |||||| | | |||| |  | |  ||   | |
cttttgtggggttcatcgtgtcagttggagaaatcatgacttttgatgaatgatgatgaatatgctgaggatatctaacgtga---gatttgtcatttccaggTTCCTCTTCATACGATTATTGAGATACAGATGGGAGTCACGGGTGTCCAAGAGAAAAGATATAAACTAATGGACTGAAATGAATTGAAGAAAAGTTCTCT

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 22
---------------------gtgagacaacgttttgcattttatatcactgctaccctagagcaccatgcgcgtattttgcatttttgctcatcatgactgaaaatttttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGACGCAGTGAACTCCACAGCAGGGATTT
                       ||||| |   || | |   |  | |  |        ||||   | ||   | |     ||    |  | | |||   |   |  |||     ||||| |||||||| || ||||| |||||||| ||||| ||| ||||||| ||||||||| | |||||||||||||||  | |  |  | ||       |   
gtaaaatctgaattagaaaatacgagactat-cttagaacgattgagctataagctttcagagagtcttggctgcaagccacacacataat-aacatattttggatgtttcaa--cagATGCCACTTCACACTATAATAGAGATACAGATGGGAGTTTCTGGTGTGCAAGAGAAACGCTACAAACTCATGGACTGAATTCAAACAACTATTACCACAA

upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 22
gtgagacaacgttttgc-attttatatcactgctaccctagagcaccatgcgcgtattttgcatttttgctcatcatga--ctgaaaatttttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGACGCAGTGAACTCCACAGCAGGGATTT
 |   ||| | ||||   | |  ||  |  | |||    |    | ||  |     ||   ||  ||    | | |  |   | |  |||     | ||| |||| |||||||| ||||| |||||||||||||| ||| ||||||| ||||||||||||||||| |||||||||  | |   || ||||| |    || 
ttaccacatcattttatgaataaattccttttctaggagaagaaaacaatccaaagttggccaagttacaccctgacaaacttaatgattcacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAAGAGAAAAGATACAAGCTCATGGACTGACTTCGCTTCACAGAATCTTTTG

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|25044722|gb|AJ420705.1|AJ420705
EST:     TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAG                         ATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
genomic: TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAGgtgagacaac ... tttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
EST: gi|86436870|gb|CI118592.1|CI118592
EST:     TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAG                         ATACCACTTCATACCATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAT
genomic: TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAGgtgagacaac ... tttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
EST: gi|58672416|gb|CK061102.1|CK061102
EST:     TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAG                         ATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
genomic: TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAGgtgagacaac ... tttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
EST: gi|88269203|gb|CI380501.1|CI380501
EST:     TGTATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAG                         ATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
genomic: TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAGgtgagacaac ... tttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
EST: gi|86539328|gb|CI179534.1|CI179534
EST:     TATATGCATATTTTGCGGATAAACCTCTGGAGGAACTTCCTAACATTGAG                         ATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
genomic: TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAGgtgagacaac ... tttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
EST: gi|88847189|gb|CI001461.1|CI001461
EST:     TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAG                         ATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
genomic: TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAGgtgagacaac ... tttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
EST: gi|58679011|gb|CK067698.1|CK067698
EST:     TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAG                         ATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
genomic: TATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAGgtgagacaac ... tttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
EST: gi|86873340|gb|CI341565.1|CI341565
EST:     AAACCACTGGAGGAACTTCCTAACATTGAG                         ATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA
genomic: AAACCACTGGAGGAACTTCCTAACATTGAGgtgagacaac ... tttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAA

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: 66 (upstream exon), 67 (downstream exon)
Score: 15

GCTGTGCTAAGAGCACTATATGCATATTTTGCGGATAAACCACTGGAGGAACTTCCTAACATTGAGgtgagacaac ... tttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGACGCAGTGAACTCCACAGCAGGGATTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccatgcgcgtattttgcatttttgctcatcatgactgaaaatttttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGACGCAGTGAACTCCACAGCAGGGATTT
                                           tttttgctcc  CT-rich tract
           tattttgcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagacaacgttttgcattttatatcactgctaccctagagcaccatgcgcgtattttgcatttttgctcatcatgactgaaaatttttgctccagATACCACTTCATACAATAATTGAGATACAAATGGGTGTTGCTGGTGTTCAAGAGAAAAGATACAAACTCATGGACGCAGTGAACTCCACAGCAGGGATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA