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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtaacaattgttctgttgatgatatacttaggaatacctagggaaacttgctactttcatcataatgtaatcaaattgttaactaattctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGTAGAATTATTGCTGGAACATGCCACAGTGCCAAGATGAATAGGACAAT

Basic information

species Oryza sativa
transcript LOC_Os08g10608.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G23740.1 (Arabidopsis thaliana), 3'ss of exon 3
-------catgtaacaattgttctgttgatgatatacttaggaatacctagggaaacttgctactttcatcataatgtaatcaaattgttaactaattctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGTAGAATTATTGCTGGAACATGCCACAGTGCCAAGATGAATAGGACAAT
       ||   |    |  ||   ||||| |  |    || || |||   | ||| |||  |  |   |  |||| |  |  |  |||| | |   | ||   ||||  | ||||| || |  ||||| |||||||||||||| ||||||||||||||  | ||  | ||||| || |||||||||||||||||| | || || ||
tgaatatcactgagtgctgtttgctttgattaggtttgaagcaaaacc---gaaaatttgagagatgttttgtaatct--ttgatatgtttattg--tgtggaacagGAGCTTACATTGACAGTAAATGTCCATTCACTGGAACCGTTTCTATCAGAGGACGTATCTTAGCTGGTACTTGCCACAGTGCCAAGATGCAGAGAACCAT

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G48930.1 (Arabidopsis thaliana), 3'ss of exon 3
catgtaacaatt--gttctgttgatgatatacttaggaatacctagggaaacttgc-tactttcatcataatgtaatcaaattgttaactaattctgttt--cagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGTAGAATTATTGCTGGAACATGCCACAGTGCCAAGATGAATAGGACAAT
     |   |||    | |||     |  | | ||| ||     |        |   ||| || |   | |  |  |||  || ||   || || |||    ||||  | ||| | || ||||||||||| ||||||||||||||||| || |||||| | ||  | ||||| || ||||||||||| || ||| | ||||| ||
----cactgatttgaatatgtgatcaagcttcatagaaacctgcatcattctctatatacctttaa-gtcagattctcaggttattgtgtatttgtgtggaacagGAGCTTACGTTGACAAGAAATGCCCCTTCACTGGAACTGTTTCCATTAGAGGTCGTATCTTAGCTGGTACTTGCCACAGTGCGAAAATGCAGAGGACCAT

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 3
catgtaacaattgttctgttgatgatatacttaggaatacctagggaaactt--gctactttcatca-taatgtaatcaaattgttaac----taattctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGTAGAATTATTGCTGGAACATGCCACAGTGCCAAGATGAATAGGACAAT
    | |||    ||| |   |   ||| ||    | |  ||||  || |||   || | ||||| |   |||    |   ||     |    |  ||  ||  |||| || || || |||||||||||||| |||||||| ||||||||||| || ||  | ||  | ||||| || ||||| |||||||||||||  ||||| ||
--gttgacaccaattcag--aaaagtattct---aattggctagctaagctttaactgccttcatgagcgatgctgacttgttcccttcgttgttgtttggtaacagGTACTTATATTGATAAGAAATGCCCCTTCACTGGCACTGTTTCTATTAGGGGCCGCATCTTAGCTGGCACTTGCCATAGTGCCAAGATGATGAGGACCAT

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 3'ss of exon 3
catgtaacaattgttctgttgatgatatacttaggaatacctagggaaacttgctactttcatcata---atgtaatcaaattgttaactaattctgttt-cagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGTAGAATTATTGCTGGAACATGCCACAGTGCCAAGATGAATAGGACAAT
   | || | | | | |   ||    | | |        || |     |||   ||   |  ||||    ||   |   || |  |||||  | || ||  |||| || ||||| || |||||||| || |||||||||  |||||||||||| ||  | ||| ||||||| || ||||||||||| |||||||  ||||| ||
---gcaa-agtagattttgagaaatcacaatgcaagcgcccaaatctgactctgtatgcttgtcatgtttataacaatgaactaataacttttgctattggcagGAACATACATTGACAAGAAATGTCCGTTCACTGGAGGTGTTTCTATCAGGGGCCGTATTCTTGCTGGTACTTGCCACAGTGCGAAGATGATGAGGACCAT

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|88569513|gb|CI660688.1|CI660688
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTCTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|33659206|gb|CF281819.1|CF281819
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|88592803|gb|CI710931.1|CI710931
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|88429254|gb|CI690148.1|CI690148
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|33661075|gb|CF292042.1|CF292042
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|58602254|gb|CK012782.1|CK012782
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|88587591|gb|CI705349.1|CI705349
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|58601143|gb|CK011671.1|CK011671
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|163918131|gb|EG713997.1|EG713997
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|58596143|gb|CK006671.1|CK006671
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATNAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|163918124|gb|EG713162.1|EG713162
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATC
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATC
EST: gi|163917913|gb|EG713965.1|EG713965
EST:     CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAG                         GGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG

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: 75 (upstream exon), 62 (downstream exon)
Score: 60

CCAAAGAAATCTGGCAAAGGGAAGAAGCCTGGCAAGGGAGGTAACCGCTTCTGGAAGAATATTGGCCTTGGCTTCAAGACACCCCGGGAAGCAATTGAAGgtaataaata ... tctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGTAGAATTATTGCTGGAACATGCCACAGTGCCAAGATGAATAGGACAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaacttgctactttcatcataatgtaatcaaattgttaactaattctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGTAGAATTATTGCTGGAACATGCCACAGTGCCAAGATGAATAGGACAAT
                                      aactaat  putative branch site (score: 60)
                                            ttctgtttc  CT-rich tract
                   ataatgtaatcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtaacaattgttctgttgatgatatacttaggaatacctagggaaacttgctactttcatcataatgtaatcaaattgttaactaattctgtttcagGGACCTACATCGATAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGTAGAATTATTGCTGGAACATGCCACAGTGCCAAGATGAATAGGACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
catgtaa
- - - - - ttgttct
- - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa