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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacatataatccattttttgttttttgaaatctgaactcttgcattgactcttatgaataataaacaacttattagttcattggacatattcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG

Basic information

species Oryza sativa
transcript LOC_Os10g28350.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g28350.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0020g04080.t01 (Vitis vinifera), 3'ss of exon 5
tacatataatccattttttgttttttgaaatct---gaactcttgcattgactctt--atgaataataa--acaacttattagttcattggacatattcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG
    |     |  | | ||||  ||  | ||||      |   | |||| | |  |  |||| ||| ||  | ||| | ||  || ||   |  |||| ||   ||||||||| | ||||||||||| |||||||||||||| ||||  || ||||| |||||  |||| ||||||||
----tgactactgtgtcttgtccttgcatatcttctatgccagttcattaaatactgtatgattaaaaaggaaaacctgtttcttaatgaaatttattttt---cagGCAATGAGGCTGTTTGTTGGTGATCCTGTTTGGACTCCCTTTAATCGTCCTCATGATAATCTACCTGCAAG
















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|33682515|gb|CF310754.1|CF310754
EST:     CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGT
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGT
EST: gi|88270931|gb|CI380231.1|CI380231
EST:     CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
EST: gi|87036234|gb|CI190856.1|CI190856
EST:     CTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
genomic: CTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
EST: gi|88509164|gb|CI436670.1|CI436670
EST:     CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
EST: gi|33693837|gb|CF322076.1|CF322076
EST:     CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
EST: gi|88489103|gb|CI426375.1|CI426375
EST:     CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
EST: gi|9865230|gb|AU100980.1|AU100980
EST:     CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
EST: gi|33682516|gb|CF310755.1|CF310755
EST:     CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
EST: gi|88275016|gb|CI395620.1|CI395620
EST:     CTGCAGGGATGTACCCCCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
EST: gi|88271996|gb|CI388049.1|CI388049
EST:     CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCC
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGC-AATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCC
EST: gi|88992645|gb|CI035679.1|CI035679
EST:     CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAG                         GCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC
genomic: CTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCC

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: 51 (upstream exon), 74 (downstream exon)
Score: 17

TGATCAGTGGATTCGTATAGCACTGAAGAAAGGAGGCATGATTGTTCTGCCTGCAGGGATGTACCACCGCTTTACGTTGGACACCGACAACTATATCAAGgtactcctct ... tcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactcttatgaataataaacaacttattagttcattggacatattcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG
 cattgac  putative branch site (score: 17)
                                          tattctttt  putative PPT
      ttatgaataataaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacatataatccattttttgttttttgaaatctgaactcttgcattgactcttatgaataataaacaacttattagttcattggacatattcttttacagGCAATGCGACTGTTTGTTGGCGATCCTGTTTGGACACCCTACAACCGTCCCCATGACCATCTTCCTGCAAG

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