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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctctattacttggaattatctatcaaaagcattctcactaatttcttatgatttcatgcaattatttcaaatgttaaatcttcttatagcagGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAGAGA

Basic information

species Oryza sativa
transcript LOC_Os01g01800.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01800.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G036206_T01 (Zea mays), 3'ss of exon 17
gtatgttctctattacttggaattatctatcaa---aagcattctcactaatttcttatgatttcatg-caattatttcaaatgttaaatcttcttatagcagGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAGAGA
   | | |||| | | ||| ||| |   ||  |   |   ||||| | || |||||| |||| |||   ||   || | || | || |||   |  | ||||||| | ||||||||| || |||||||||||| || | ||||||||||||||||| ||||| |||||||||| ||| |||||||||||| |  ||||||   
--gtatgctctgtcatttgcaatcacacattcactcatcaattcttattactttcttctgatgtcacaacaccgatctgaactattgaattccccaacagCAGGTCAGATTTTTAGACATATGGGAACCAGCTGTTCTAGCAATAAAGAGGGAAGGTTACAGCATTAAATGTAATGGGCAGCGTGGTGTTCTAATCACAG---

upper sequence: LOC_Os01g01800.2 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
-----------------------------gtatg-ttctctattacttggaattatctatcaaaagcattctcactaatttcttatgatttcatgcaattatttcaaatg-------ttaaatcttcttata--gcagGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAGAGA
                              |||  |||| | ||  |     ||  |||||||| |  || |||  ||  | |  |  ||| ||   |   | | |||          | |||||| | ||   |||||    || | | ||||| ||||||||||||| |||||| || ||||||||||| ||||| || || |||||||| |   |||||| |||  || | ||||
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaa-gtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA
















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|29628866|gb|CB633877.1|CB633877
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|29628866|gb|CB633877.1|CB633877
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|29628866|gb|CB633877.1|CB633877
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|29628866|gb|CB633877.1|CB633877
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|32947857|gb|BP184429.1|BP184429
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|32947857|gb|BP184429.1|BP184429
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|32947857|gb|BP184429.1|BP184429
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|32947857|gb|BP184429.1|BP184429
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|86437315|gb|CI119037.1|CI119037
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|86437315|gb|CI119037.1|CI119037
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|86437315|gb|CI119037.1|CI119037
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-
EST: gi|86437315|gb|CI119037.1|CI119037
EST:     TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCT                         C
genomic: TTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcag-

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: 38 (upstream exon), 59 (downstream exon)
Score: 4

ATCCTGAAACAAAGGAGCTTATTAAGAGAACTCTTGAAACTGGTCATGTATCTTATGAAGTCCAACTACCTgtatgttctc ... cttatagcagGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAGAGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatttcttatgatttcatgcaattatttcaaatgttaaatcttcttatagcagGTGAAATTTTTAGATATGTGGGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAGAGA
                                         tcttcttat  CT-rich tract
                      aattatttcaaatgtt  TA-rich tract