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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcattttttttgggtgacaatgtatataacctagctgtagttattaataggagcttttttgaccctctgttgtgattcataaaagtttctaataggatgtaatcaccaccaattaacattgtagtgacagtattgcttcctgatgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG

Basic information

species Oryza sativa
transcript LOC_Os01g64660.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G836250_T03 (Zea mays), 3'ss of exon 8
-------------gtgatcattttttttgggtgacaatgtatataacc-tagctgtagttattaataggagcttttttgaccctc------tgttgtgattcataaaagtttctaataggatgtaatcaccaccaattaacattgtagtgacagtattgcttcctgatgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG
               |||| ||   | | | |  | |    || ||   |   || |  |||  ||  |  | |||        |      || ||  | |  | | || ||   |  | |    |  |  ||  | ||       |  ||   |  || ||     | |||  ||||||||||||||| || |||||||| |||||||| || || || |||||||||||||| ||| |||||| |||||| ||||| |||||
gtgagtcgatcgatcgatctttcactatagatctccaccagtacaaaaatgaatgaacgtatgcatgcggccgtttacatatgacgaaggatgatggtactgttgatagctttatactgca-acgactaaaacacactactcgctgatcgatgctgatggtttgcttttattaacagTATGGTTGCTGACGTGCACCGTACCTTGCTATACGGCGGTGTGTTTTTGTACCCTGCTGACGAGAAGAACCCAAACGGAAAGCTCCG

upper sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 10
gtgatcattttttttgggtgacaatgtatataacctagctgtagttattaataggagcttttttgaccctctgt-tgtgattcataaaagtttctaataggatgtaatcaccaccaattaacattgtagtg-acagtattgcttcctgatg-atttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG
                                                          | |  ||| |  |||| |      | | || ||  | |  || |||  | ||  |  || |    || |  |  | | |||  | ||   ||  ||   ||| ||||| |||||||| || ||||||||||| ||||||||  | |||||||||||||| ||||| || || |||||||||||||| ||
---------------------------------------------------------ttctcatgaactactgtctactgcacttgaatgtggcca-cagaatg--accaagattaactttttttttcttccaaattatgacatctgtatacatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG

upper sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
gtgatcattttttttgggtgacaatgtatataacctagctgtagttattaataggagcttttttgaccctctgttgtgattcataaaagtttct--aataggatgtaatcacca----ccaattaacattgtagtgacag-tattgcttcctga-tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG
                                                                  | || ||||| |  | ||  |  | | |  |||  |||||  |  |      ||||  |  ||| |  | |    || |  | |  || |||||| ||| ||||| |||||||||||||| || || || || || ||  | |||||||||||||| || ||||||||||| || |||||||| ||
-----------------------------------------------------------------gctctttgttgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttacagCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG

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|38470545|gb|CF954676.1|CF954676
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|29686739|gb|CB683014.1|CB683014
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|29621610|gb|CB626621.1|CB626621
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|38473796|gb|CF957928.1|CF957928
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|58588683|gb|CF986991.1|CF986991
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|86413542|gb|CI019127.1|CI019127
EST:     TGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: TGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|58590217|gb|CF988525.1|CF988525
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|89184643|gb|CI007068.1|CI007068
EST:     TCCCTAAGGATGGTTCATCACCTAAATCCTTGACG-TACATTGGAAG                         TATGTTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: TCCCTAAGGATGGTTCATCACCTAAATCCTTGA-GATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|29613014|gb|CB618027.1|CB618027
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|88967746|gb|CI016261.1|CI016261
EST:     TGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: TGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|29617760|gb|CB622772.1|CB622772
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|33820806|gb|CF336207.1|CF336207
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|4714676|gb|AU055793.1|AU055793
EST:     AAGTNCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|27546650|gb|CA764792.2|CA764792
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|89198621|gb|CI016706.1|CI016706
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|86874736|gb|CI318295.1|CI318295
EST:     ATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: ATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|29682614|gb|CB678889.1|CB678889
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
EST: gi|38476585|gb|CF960718.1|CF960718
EST:     AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACA-TGGAGG                         TATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA
genomic: AAGTTCCCTAAGGATGGTTCATCACCTAAATCCTTGAGATACATTGGAAGgtgatcattt ... tgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatcaccaccaattaacattgtagtgacagtattgcttcctgatgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG
            aattaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatcattttttttgggtgacaatgtatataacctagctgtagttattaataggagcttttttgaccctctgttgtgattcataaaagtttctaataggatgtaatcaccaccaattaacattgtagtgacagtattgcttcctgatgatttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG