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'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaatctggattatttacgcacataaatatgctcagttttacctacctgctctgtataccaggtccaggggcaagcaatttgtgcatatgattgttactaactttttatgtttgctattgactcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTCATGACTAATGACATAACTGACAACCCTGAAGAAGCTGTCCATTGCTTTG

Basic information

species Oryza sativa
transcript LOC_Os03g14980.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G550865_T02 (Zea mays), 3'ss of exon 6
gttaaatctggattatttacgcacataaatatgc-tcagttttacctacctgctctgtataccaggt---ccaggggcaagcaatttgtgcatatgattgttactaactttttatgtttgctattgac---tcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTCATGACTAATGACATAACTGACAAC---CCTGAAGAAGCTGTCCATTGCTTTG
|| | ||| |  |  | |   || ||| || ||| | | |  |    |  |      | | |   |     ||  ||  |  | | |||      |||||||||||| || ||  |||||||||| |    |||| ||||| |  || ||||| |||||   | |||||||||| ||||| |||||  | |||||||||||||  |||||||||   |||||||||||||| || ||||   
gtgagatccgattcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctctgcatatcattggtgaaaattgtgtatggtagattgttactaaattgttcagtttgctattcatcaatcttatagGCAAGCGCGAGTGTGTCTCCCACACTATGGCAACCACCAAGTGGCATTTTGATGACTAATGACACGACTGACAACAATCCTGAAGAAGCTGTTCACTGCT---

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 21
gttaaatctggattatttacgcacataaatatgctcagtt--ttacctacctgctc-tgtataccaggt-ccaggggcaagcaatttgtgcatatgattgttactaactt-tttatgtttgctattgac---tcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTCATGACTAATGACATAACTGACAAC---CCTGAAGAAGCTGTCCATTGCTTTG
|| | |||||  |  | |   || ||| || |||  |  |  |   |     |||| | |     |  | |||  || ||  | ||||||     |||||||||||| ||  | |  ||| ||||| |    |||| ||||| || |||||||| |||||     |||||||||| ||||| |||||| | |||||||||||||  ||||||||    |||||||||||||| || ||||   
gtgagatctgtttcttatgtacatatagatgtgcataaatagtgttcagatcgctcatcttctttacataccataggtaaaaattttgtgtggtagattgttactaaattgctcaatttttctattcatcaatcttatagGCAACCGCAAGTGTATCTCCCACTCTATGGCAACCACCAAGTGGCATCTTGATGACTAATGACACGACTGACAATAATCCTGAAGAAGCTGTTCACTGCT---
















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|88348934|gb|CI653978.1|CI653978
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|58658403|gb|CK047083.1|CK047083
EST:     TCATCTGCTCTGGAAATGGGGGTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TCATCTGCTCTGGAAAT-GGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|88344056|gb|CI638791.1|CI638791
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|58657128|gb|CK045808.1|CK045808
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|58655231|gb|CK043911.1|CK043911
EST:     TCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|58691548|gb|CK080235.1|CK080235
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|58659010|gb|CK047690.1|CK047690
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|58658854|gb|CK047534.1|CK047534
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|58656462|gb|CK045142.1|CK045142
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|88573729|gb|CI665498.1|CI665498
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|29680680|gb|CB676955.1|CB676955
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|58694923|gb|CK083610.1|CK083610
EST:     -TCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
EST: gi|29673860|gb|CB670135.1|CB670135
EST:     TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAG                         GCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC
genomic: TTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTC

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: 72 (upstream exon), 65 (downstream exon)
Score: 30

TATTTACACAAATTCTGGTGTCGCTATCTTGGCTTTAGCTTCAAATGCTGTTCATCTGCTCTGGAAATGGCCTCGCAATGACCGAAACTCAAGTGGAAAGgttaaatctg ... actcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTCATGACTAATGACATAACTGACAACCCTGAAGAAGCTGTCCATTGCTTTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttgtgcatatgattgttactaactttttatgtttgctattgactcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTCATGACTAATGACATAACTGACAACCCTGAAGAAGCTGTCCATTGCTTTG
                                              ctcttct  CT-rich tract
                   ttactaactttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaatctggattatttacgcacataaatatgctcagttttacctacctgctctgtataccaggtccaggggcaagcaatttgtgcatatgattgttactaactttttatgtttgctattgactcttctagGCTACTGCAAGTGTTTCTCCTCAATTATGGCAACCTCCAAGCGGCATCCTCATGACTAATGACATAACTGACAACCCTGAAGAAGCTGTCCATTGCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG