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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgccatatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA

Basic information

species Oryza sativa
transcript LOC_Os03g06410.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G038982_T01 (Zea mays), 3'ss of exon 6
gtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgattt-ttgctgcaatgttttgatttgcc-atatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA
|||||||||  | ||| | |||    |||||| ||| |||  |   || |      ||||| ||||      |  | | |  | || |||||  | ||||| ||| | |  || |||||| | |  ||||||| || ||||||||||| ||||| |||||||||||||||||||| |||||||||||||| || ||||| |||||||||||||||||||| || |||||||
gtaggtgaacttttatctgtttc---tatcttggagttttcgtaaataaat----aattcaattatcatatttactcagtccagttgttgctttattgttt-gatatacggatgtactttatctg-acaagGTCCGAATTATGCGTCGGCTGCGCCATCCAAATATTGTTCTCTTTATGGGTGCTGTTACACGCCCTCCGAACTTATCTATTGTATCTGAATACCTTCCAA

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G175563_T01 (Zea mays), 3'ss of exon 6
gtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgcc-atatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA
|||||||||  | ||| | |||    |||||| ||| ||| ||   || |   |   |  ||||   | |    |    |  ||| ||| |  | ||||| ||| | |  |||||||||   || ||||||| || ||||||||||| ||||| |||||||||||||||||||| |||||||||||||| || ||||| |||||||||||||||||||| ||||||||||
gtaggtgaacttttatctgtttc---tatcttggagttttcctaaataaactat---tcaattttcatatttactcagttcaattgttgatttattgttt-gatatacggatatacttt---ttgacaagGTTCGAATTATGCGTCGGCTGCGCCATCCAAATATTGTTCTCTTTATGGGTGCTGTTACACGCCCTCCGAACTTATCTATTGTATCTGAATATCTTCCAA

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 7
gtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgcc-atatactttcttt-ttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA
                                | ||  | | | |  |    |||  |||||   |  |   |     ||   | | | ||  || |     |||   |  | || |   |||  | |||||||||||| |||||| | || |||||||||||||||||||| || ||||||||||||||||||||||| ||  | || ||  | || |||||||| ||||
------------------------------gaaaagaataagttgacaggcagtgatttcatgggtaagg-gtccaccatgattatcttcttaaaggccaaaattaatctgtttaatccttttgctgcaagGTGCGGATAATGCGTAGGCTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTGTCAATCATTTCAGAGTATCTACCAA

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 7
gtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgcca--tatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA
                                | ||  | | | |  | |  |||| ||||||   | |   |     ||   | | | |   || |     | |   |   | ||  || ||  |  ||||| ||||| |||||| |  | |||||||||||||||||||| || ||||||||||||||||||||||| ||  | || ||  | || |||||||| ||||
------------------------------aaaaagaataagttgacagacagtggtttcatt-ggtagaggtccaccatcattatcttcctaaaggccaaaactaatctgttttatctttttgctgaaagGTACGGATAATGCGTAGGTTACGTCATCCAAATATTGTTCTTTTTATGGGTGCTGTTACTCGTCCTCCCAATCTCTCAATCATTTCAGAGTATCTACCAA

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 6
-------gtaggtgaaactatatatattttata-tat-cttagagctttactggctatagcg--tggattcatttatttgtcatttttaattgatt-tttgctgcaatgttttgatttgccatatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA
        || ||  |  |   | |||||  || ||| |||||      | |   | |   |  || |  || |   ||  | ||     ||  ||  ||||       ||   | |      ||| || | | |   ||||| |||||||||||  || |||||||||||||| ||||  ||||| | || ||||||||||||||||||||  | || || ||  | |||| ||| || |
gtaagccataagttcacttgcgtttatttactagtatacttagctacccatttatttttttggttgaacccaatggctta-cgttgcagcttatttgcttgcctttgaattcccactctattaatatttccctatctgaagGTACGGATTATGCGAAGATTGCGTCATCCAAATGTTGTATTCTTCCTTGGGGCTGTTACTCGTCCTCCAAATCTTTCCATCGTCACAGAGTTTCTGCCTA

upper sequence: LOC_Os03g06410.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 6
gtaggtgaaactatatatattttatatatcttagag-ctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgccatatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA
       ||| ||| |||||| | | ||| || ||| |||  ||||  ||   ||      ||  |      || || | ||||| | ||      | |||||             ||  ||  |  |||||||| || |||||| || | |||||||||||| ||||||| || ||||||||||||||||| ||||||||| | |||||  |  |||||| ||||||||
-------aaaatat-tatattatttctatgttggagacttggctggtaattttgt-----tataaagcaaaaatgttaacttgatgtctgtc----ttttttg-------------ttctttaatgtaagGTGCGAATAATGCGTAGATTACGTCATCCAAATGTTGTTCTTTTTATGGGTGCTGTTACTCGCCCTCCAAACCTCTCTATCATCACTGAGTTTCTTCCAA

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|88571349|gb|CI662722.1|CI662722
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|569642|gb|D40491.1|D40491
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|2799344|gb|AA752333.1|AA752333
EST:     AGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: AGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|58596848|gb|CK007376.1|CK007376
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|569641|gb|D40490.1|D40490
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|571627|gb|D41138.1|D41138
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
EST: gi|58688165|gb|CK076852.1|CK076852
EST:     TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAA                         GTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT
genomic: TCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGT

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: 69 (upstream exon), 70 (downstream exon)
Score: 25

GAAGTAGCTGTCAAGAAATTCTTGGATCAAGATTTCTATGGTGATGCTTTGGATGAATTCCGGAGTGAAgtaggtgaaa ... tttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaattgatttttgctgcaatgttttgatttgccatatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA
                                    tatactttcttttt  CT-rich tract
                                   atatactttcttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtgaaactatatatattttatatatcttagagctttactggctatagcgtggattcatttatttgtcatttttaattgatttttgctgcaatgttttgatttgccatatactttctttttacaagGTGCGGATTATGCGTCGACTGCGTCATCCAAATATTGTTCTCTTCATGGGTGCTGTTACTCGTCCTCCAAACTTATCTATTGTATCTGAGTATCTTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT