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

...ctgtacatgcttgctatgttggaacttatcacgttcgctgttattgtgtggcggttgataaccattgagcttaccacaaaaactgttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC

Basic information

species Oryza sativa
transcript LOC_Os02g17320.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 15
-ctgta-catgcttgctatgttggaacttatcacgttcgc---tgttattgtgtggcggttgataaccattgagcttaccacaaaaactgttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC
 | | | ||   |||  |     | |  | | | ||  |    || |   |||| |||  |  |  |     |   || | ||  |  |        | || ||||| |||||||||||||||||||| ||||||||||| || |||||||||||||| || || || || ||||||||||| |||||||||||||| ||  | |
acagaagcaattttgtaacaactgtatctgtgaagtgtgtacatgatggcgtgtagcgcgtagtggcttggaaatctaactcatcagttt-----gctcttacagGCGCCCCAAGGAGTGCATGTGGTGAGCAAGAGATTCCCTAGAGTGAAGATCGTTACTTCGGAGATTGAGTTTGGTCTAAATGATGATTTCCGTGTTGTGC

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 13
ctgtacatgcttgctatgttggaacttatc-acgttcgctgttattgtgtggcggt-tgataac-cattgagcttaccacaaaaact----gttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC
      ||| |   | |  |   ||| ||  |   ||  |||| |    ||  ||  || ||   ||| | | ||   |    ||||    | ||| | | || ||||| ||||||||||||||||||||  |||||||||| || ||| |||||||||| || || || || ||||  ||||| |||||||||||||| ||| | |
------atgatgtgtgtaatcagactcatttatcatcattgttgt-acatgatggcatgttagtgcatagtggttggaaatctaactcgtcggtggtactcttacagGCGCCCCAAGGAGTGCATGTGGTGTGCAAGAGATTCCCTAGAATGAAGATCGTTACTTCGGAGATTGAGTCCGGTCTAAATGATGATTTCCGTGTCGTAC

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 14
-----------------------------ctgtacatgcttgctatgttggaacttatcacgttcgctgttattgtgtggcggttg--ataaccattgagcttaccacaaaaactgttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC-
                              |       |||  |   ||| ||  |      ||| || ||  |   |     ||   ||     ||  | ||  ||    |  | || | |   || ||||| ||  |||| |||||||||||  |||| || ||||||||| | ||||| || ||||| || || ||| ||||| ||||||| |||||||| ||||| | 
taagtgactattgtcttggttcctctatatttcttgctctttttcctttgcaatgtgattaattctctcttgcttctttctttttattatgttgtttatgattttcatttga--tttttgcaccttttcaggCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTAACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATACC

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 14
-------------------------ctgtacatgcttgctatgttggaacttatcacg-----ttcgctgttattgtgtggcggttgata-accattgagcttaccacaaa--aactgttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC
                         |||||  | |||||||  ||     |||    |     ||| || ||  |   |     ||  |    | || |  |       |    |  | ||    | || ||||| ||  |||| |||||||||||  |||| || ||||||||| | ||||| |||||||| || || ||| ||||| ||||||| |||||||| ||||| |
gtaagtgactaatgtcttagttcctctgtatct-cttgctaattttctttttactgtgattaattctctcttgcttctttctttttattgtgtcgtttaaatggttttcatttgatcgctgctcct-tttcagGCACCTAAAGGTGTGCATGTGGTATGCAAAAGTTTTCCAAGAATAAAGATAGTGACATCGGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC

upper sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 11
---------------------------ctgtacatgcttgctatgttggaacttatca--cgttcgctgtta-ttgtgtggcggttgataaccattgagcttaccacaaaaac-tgttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC
                           || |  ||      ||| |||  | || |      ||  |||||  || | |      |  || | | |||  |    | | | |  || |   ||  | |||||| || ||||| || ||||||||| | || |||||||||||| | || ||| ||||||| || || ||| ||||| ||||||| |||||||| ||||| |
gtaagttacttgtgcctgttgttgttcctctgtatatcatatatcttgccatttctttgttattttctgttgcttctttcttttcttgtacctaatgatttgcatatatatatatgctctcatattgccagGCACCTCAAGGTGTTCATGTGGTCTGTAAAAGATTTCCAAGAATAAAAATCCTGACATCTGAGATTGAGATTGGTTTGAATGAAGATTTCCGTGTCATAC

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|88273348|gb|CI388804.1|CI388804
EST:     CTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: CTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|29633369|gb|CB638378.1|CB638378
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|86886699|gb|CI334613.1|CI334613
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|87037876|gb|CI192498.1|CI192498
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|3760815|gb|C98069.1|C98069
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|33683400|gb|CF311639.1|CF311639
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTA-TTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|87029276|gb|CI276544.1|CI276544
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|88233330|gb|CI233179.1|CI233179
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|86843464|gb|CI339536.1|CI339536
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|86498530|gb|CI141163.1|CI141163
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|86505781|gb|CI148414.1|CI148414
EST:     ATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: ATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|29675373|gb|CB671648.1|CB671648
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|29627016|gb|CB632027.1|CB632027
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|86537180|gb|CI177386.1|CI177386
EST:     TGAAAAAGGGTGTACAGGAAACAAATATCATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|29669519|gb|CB665794.1|CB665794
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|29643326|gb|CB648333.1|CB648333
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|86536638|gb|CI176844.1|CI176844
EST:     TGAAAAAGGGTGTACAGGAAACAAATATCATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
EST: gi|86486730|gb|CI129363.1|CI129363
EST:     TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCA                         GCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC
genomic: TGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATC

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: 71 (upstream exon), 71 (downstream exon)
Score: 21

GAAATTCAGCTGTTCAAGCTATATCTCTACTCTTGAAAAAGGGTGTACAGGAAACAAATATTATTTTTCTGAATCTTATATCAgtaagtctac ... attgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtggcggttgataaccattgagcttaccacaaaaactgttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC
                                              ttgttcc  CT-rich tract
         ttgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtacatgcttgctatgttggaacttatcacgttcgctgttattgtgtggcggttgataaccattgagcttaccacaaaaactgttggaattgttccagGCTCCCCAAGGAGTGCATGTGGTCAGCAAGAGATTTCCAAGAGTGAAGATCGTGACATCAGAAATCGAGTTTGGTCTGAATGATGATTTCCGCGTCATCC

ctgtaca
- - - -tgcttgc
- - - - - - - tatgttg
- - - - - - - - - - - - - - - - - -cgctgtt
- - - - - - - - - - - - - - - - - - - - - - - tgtggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgg