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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCCCTGTCTACAGTCCACCTGCTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagttcatattaagattctagaataatatgcacatgtttcaccgctctcaaaacattggggattcatctttgtctgcag

Basic information

species Oryza sativa
transcript LOC_Os02g48110.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g48110.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G137696_T01 (Zea mays), 5'ss of exon 1
---------------------------CACCCCTGTCTACAGTCCACCTGCTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagttcatattaagattctagaataatatgcacatgtttcaccgctctcaaaacattggggattcatctttgtctgcag
                            ||||||||||| ||  |||| | ||||||||||||| |||| || || |||||||||||| |||||||||||||||| || ||  || |          || | | |||| ||   |||  ||  | |  | ||        | | ||  | |||||
GGCTAACTCCGGTTGAGCATTTTGCAGTACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAAAGTTCTGGACTTACAAGATAAGgttagtaatttggtagtggacccaacaaaaagtctgcatattactcatggcagtaatcatatctata--cccttttattgtgcag

upper sequence: LOC_Os02g48110.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G020040_T02 (Zea mays), 5'ss of exon 13
CACCCCTGTCTACAGTCCACCTGCTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagttcatattaagattcta-gaataatatgcacatgtttcaccgctctcaaaacattggggattcatctttgtc-tgcag
 ||||||||||  |  ||||| | |||||||||||||||||| |  || |||||||||||| |||||||||||||||| || ||  ||  || |  |||  || |||    | |    ||       | |  ||| ||   || |   ||  |   ||||
TACCCCTGTCTTTAACCCACCAGTTTTCACATCTGAAGAAGTTTCTGAGAAAGTTCTGGACTTACAAGATAAGgttagtaatttggtagaaacaccctataaaaaatcccgagactgctcgtgaaagtaattacaatgtatatactctttcattgcgcag

upper sequence: LOC_Os02g48110.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G020040_T01 (Zea mays), 5'ss of exon 12
---------------------------CACCCCTGTCTACAGTCCACCTGCTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagttcatattaagattcta-gaataatatgcacatgtttcaccgctctcaaaacattggggattcatctttgtc-tgcag
                            ||||||||||  |  ||||| | |||||||||||||||||| |  || |||||||||||| |||||||||||||||| || ||  ||  || |  |||  || |||    | |    ||       | |  ||| ||   || |   ||  |   ||||
GGCTAACTCCCATTGAGCATTTTGCAGTACCCCTGTCTTTAACCCACCAGTTTTCACATCTGAAGAAGTTTCTGAGAAAGTTCTGGACTTACAAGATAAGgttagtaatttggtagaaacaccctataaaaaatcccgagactgctcgtgaaagtaattacaatgtatatactctttcattgcgcag

upper sequence: LOC_Os02g48110.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G137696_T02 (Zea mays), 5'ss of exon 10
CACCCCTGTCTACAGTCCACCTGCTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagttcatattaagattctagaataatatgcacatgtttcaccgctctcaaaacattggggattcatctttgtctgcag
 ||||||||||| ||  |||| | ||||||||||||| |||| || || |||||||||||| |||||||||||||||| || ||  || |          || | | |||| ||   |||  ||  | |  | ||        | | ||  | |||||
TACCCCTGTCTATAGCTCACCAGTTTTCACATCTGAACAAGTTTATGAGAAAGTTCTGGACTTACAAGATAAGgttagtaatttggtagtggacccaacaaaaagtctgcatattactcatggcagtaatcatatctata--cccttttattgtgcag

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|27554442|gb|CA998342.1|CA998342
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGAT
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGAT
EST: gi|27576359|gb|CA999053.1|CA999053
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAAACCAAA-CCCAAGATAGAAAAGAA
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAA-CCAAAACCCAAGATAGAAAAGAA
EST: gi|86481739|gb|CI124372.1|CI124372
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAACCNAAACCCAAGATAGAAAAGAAA
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
EST: gi|29673173|gb|CB669448.1|CB669448
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
EST: gi|66914322|gb|CX101170.1|CX101170
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
EST: gi|86855845|gb|CI271064.1|CI271064
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAACCNAAACCCAAGATAGAAAAGAAA
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
EST: gi|29673174|gb|CB669449.1|CB669449
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
EST: gi|27576406|gb|CA999100.1|CA999100
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
EST: gi|58663600|gb|CK052286.1|CK052286
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
EST: gi|33800174|gb|CF325951.1|CF325951
EST:     CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAG                         GTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA
genomic: CTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAA

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: 64 (upstream exon), 75 (downstream exon)
Score: 53

CACCCCTGTCTACAGTCCACCTGCTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagt ... ttgtctgcagGTTTCTAGTGTCAATAGGATACCTAAACCAAAACCCAAGATAGAAAAGAAACCTCCCAAGGAAGAAGAGTCTGCTAACAAAGAGAAAACTGACTCTTCGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCCCTGTCTACAGTCCACCTGCTTTCACATCTGAAGAAGTCTACGAAAAAGTTCTGGACCTACAAGATAAGgttaggaagttcatattaagattctagaataatatgcacatgtttcaccgctctcaaaacattggggattcatctttgtctgcag

- - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - AGAAGT