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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatttaagtttgcagtggcttgcattttttggtggatttctagtattgctctattacaagttacaacttgattgacatgtccgttgcttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g45650.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 12
tttcatttaagtttgc--agtggcttgcattttttggtggatttctagtattgctctattacaagttacaacttgattgacatgtccgttgctt-gattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG
    ||| |||||  |        ||  || |  || |   |   |  | |||   |  |  |  |||   || ||||||    |  ||| ||| ||||| ||||||| | ||||||  |||| ||||||||||| ||||| ||||||||||||||  | |||||||||||||||
---gattcaagttgccttgaaaatttagatgtggtgttctctgattttttttggcattatgaacattattgctcgattgatgcatgtgttactttgattgcagCACACCAGAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G305559_T01 (Zea mays), 3'ss of exon 2
tttcatttaagtttgcagtggcttgcattttttggtggatttctagtattgctctattacaag--ttacaacttgattgacatgtccgttgctt-gattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG
    ||| ||||| ||  ||       |  | |||||   |   | |||      ||||  |   |||   || ||||||    |  ||| ||| ||||| ||||||| ||||||||  |||| ||||||||||| ||||| || |||||||| ||  | |||||||||||||||
--cgattcaagtt-gccttgaaaattttgatgtggtgttctctgaatatcttggcattatgaacattattgctcgattgatgcatgtgttactttgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTAAACCTTGTTAGCAGAGCATTTGAATTTCAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 11
tttcatttaagtttgcagtggcttgcattttttggtggatt--tctagtattgctc--tattacaa--gttacaacttgattgacatgtccgttgctt-gattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG
       |  |||     || |||| |  ||| | ||   |  ||||  | |  |    |||| |    |||   || ||||||    |  ||  ||| ||||| ||||||| ||||||||  |||| ||||||||||| ||||| ||||||||||||||  | |||||||||||||||
-------ttggttcaacatgccttgaaaatttagatgtgctgttctatgagtttttggcattatagtcattattgctcgattgatgcatgtgtcacttcgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G481395_T01 (Zea mays), 3'ss of exon 2
tttcatttaagtttgcagtggcttgcattttttggtggatttctagtattgctctattacaag--ttacaacttgattgacatgtccgttgctt-gattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG
    ||| ||||| ||  ||       |  | |||||   |   | ||||     ||||  |   |||   || ||||||    |  ||| ||| ||||| ||||||| ||||||||  |||| ||||||||||| ||||| ||||||||||| ||  | |||||||||||||||
--cgattcaagtt-gccttgaaaattttgatgtggtgttctctgaatattttggcattatgaacattattgctcgattgatgcatgtgttactttgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTTAGCAGAGCATTTGAATTTCAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G422539_T01 (Zea mays), 3'ss of exon 2
tttcatttaagtttgcagtggcttgcattttttggtggatttctagtattgctctattacaag--ttacaacttgattgacatgtccgttgctt-gattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG
    ||| ||||| ||  ||       |  | |||||   |   | ||||     ||||  |   |||   || ||||||    |  ||| ||| ||||| ||||||| ||||||||  |||| ||||||||||| ||||| ||||||||||| ||    |||||||||||||||
--cgattcaagtt-gccttgaaaattttgatgtggtgttctctgaatattttggcattatgaacattattgctcgattgatgcatgtgttactttgattgcagCACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTTAGCAAAGCATTTGAATTTCAG

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|88215064|gb|CI214913.1|CI214913
EST:     GTTTCGAGGATCAGCCTGTAATAATTGGGCTGATCATATTTCAG                         CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
genomic: GTTTCGAGGATCAGCCTGTAATAATTGGGCTGATCATATTTCAGgtatgtttac ... ttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
EST: gi|88831123|gb|CI080547.1|CI080547
EST:     GGATCAGCCTGTAATAATTGGGCTGATCATATTTCAG                         CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
genomic: GGATCAGCCTGTAATAATTGGGCTGATCATATTTCAGgtatgtttac ... ttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
EST: gi|88248064|gb|CI246682.1|CI246682
EST:     GTTTTGGTTTCGAGGATCAGCCTGTAATAATTGGGCTGATCATATTTCAG                         CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
genomic: GTTTTGGTTTCGAGGATCAGCCTGTAATAATTGGGCTGATCATATTTCAGgtatgtttac ... ttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
EST: gi|86903727|gb|CI300581.1|CI300581
EST:     ATAATTGGGCTGATCATATTTCAG                         CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
genomic: ATAATTGGGCTGATCATATTTCAGgtatgtttac ... ttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
EST: gi|86259979|gb|CI065852.1|CI065852
EST:     GTTTTGGTTTCGAGGATCAGCCTGTAATAATTGGGCTGATCATATTTCAG                         CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
genomic: GTTTTGGTTTCGAGGATCAGCCTGTAATAATTGGGCTGATCATATTTCAGgtatgtttac ... ttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
EST: gi|86490395|gb|CI133028.1|CI133028
EST:     GCCTGTAATAATTGGGCTGATCATATTTCAG                         CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
genomic: GCCTGTAATAATTGGGCTGATCATATTTCAGgtatgtttac ... ttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
EST: gi|88223219|gb|CI223068.1|CI223068
EST:     AGGATCAGCCTGTAATAAGTGGGCTGATCATATTTCAG                         CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
genomic: AGGATCAGCCTGTAATAATTGGGCTGATCATATTTCAGgtatgtttac ... ttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
EST: gi|58661916|gb|CK050596.1|CK050596
EST:     TGGGTTTCCCGAGGATCAGCCTGTAATAATTGCGGCTGATCATATTTCAG                         CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC
genomic: TGG-TTTC--GAGGATCAGCCTGTAATAATTG-GGCTGATCATATTTCAGgtatgtttac ... ttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTC

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: 74 (upstream exon), 69 (downstream exon)
Score: 40

ACAATTTGGAGGATATACGCTAGTAAGGAACTCCAAAGACCTTTTTGAAAGTTTTGGTTTCGAGGATCAGCCTGTAATAATTGGGCTGATCATATTTCAGgtatgtttac ... ttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattgctctattacaagttacaacttgattgacatgtccgttgcttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG
         tattacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcatttaagtttgcagtggcttgcattttttggtggatttctagtattgctctattacaagttacaacttgattgacatgtccgttgcttgattgtagCACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAG

tttcatt
- - - - - gtttgca
- - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtcc