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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcataaaacttatttcatctactcgaatacaattttgtgacattagatacatttgttacgtgctcatgtgtacttagtatcatgtgttcctttatattagactactatcagagtaattttgcagtatatgtcagcctgtaaaaagaaaaaagaacatcagttccaaggttttctaatatgtgattttcaattgcagAATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGTACAGTGATGTATATGGTCAG

Basic information

species Oryza sativa
transcript LOC_Os04g35260.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g35260.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G013283_T01 (Zea mays), 3'ss of exon 26
gtcataaaacttatttcatctactcgaatacaattttgtgacattagatacatttgttacgtgctcatgtgtacttagtatcatgtgttcctttatattagactactatcagagtaattttgcagtatatgtcagcctgtaaaaagaaaaaagaacatcagttccaaggttttc--taatatgtgattttcaattgcagAATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGTACAGTGATGTATATGGTCAG
||||||||   ||  |       |  | | ||  |||   |          ||||| ||  |  |  ||||||  ||| || ||   || ||||||| |    |    |   |     ||||     || || ||  | ||  | ||||      |  | | |   ||||||    |||  ||   |||| |||| |||||||| | || |||||| | ||||||||||| ||||||||||||||| ||||| |||||| | ||| ||||
gtcataaa--ctacctt------tttagtgcaccttttctat--------tatttggtaacttttggtgtgtatctagcattata--ttgctttatactgatttttccttgtacatgatttgtgtagtaggt-agattatattatgaaa------ctgctgctggcaggtttctaataagctggtttttttaatttcagAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGTACTGTGATGCACATGATCAG

upper sequence: LOC_Os04g35260.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G013283_T02 (Zea mays), 3'ss of exon 26
gtcataaaacttatttcatctactcgaatacaattttgtgacattagatacatttgttacgtgctcatgtgtacttagtatcatgtgttcctttatattagactactatcagagtaattttgcagtatatgtcagcctgtaaaaagaaaaaagaacatcagttccaaggttttc--taatatgtgattttcaattgcagAATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGTACAGTGATGTATATGGTCAG
||||||||   ||  |       |  | | ||  |||   |          ||||| ||  |  |  ||||||  ||| || ||   || ||||||| |    |    |   |     ||||     || || ||  | ||  | ||||      |  | | |   ||||||    |||  ||   |||| |||| |||||||| | || |||||| | ||||||||||| ||||||||||||||| ||||| |||||| | ||| ||  
gtcataaa--ctacctt------tttagtgcaccttttctat--------tatttggtaacttttggtgtgtatctagcattata--ttgctttatactgatttttccttgtacatgatttgtgtagtaggt-agattatattatgaaa------ctgctgctggcagGTTTCTAATAAGCTGGTTTTTTTAATTTCAGAATGGTGATAAATCTGCTCGTCAGTTTTGCCATTCATTCTACTTGAATAGTACTGTGATGCACATGATC--
















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|58675083|gb|CK063770.1|CK063770
EST:     AATGGTTATTGCATACAATAAGTGGTCTCGCATACTAAGAGAG                         AATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGT
genomic: AATGGTTATTGCATACAATAAGTGGTCTCGCATACTAAGAGAGgtcataaaac ... tcaattgcagAATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGT
EST: gi|33794147|gb|CF322964.1|CF322964
EST:     ACCTGTTAATGGTTATTGCATACAATAAGTGGTCTCGCATACTAAGAGAG                         AATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGT
genomic: ACCTGTTAATGGTTATTGCATACAATAAGTGGTCTCGCATACTAAGAGAGgtcataaaac ... tcaattgcagAATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGT

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: 63 (upstream exon), 68 (downstream exon)
Score: 7

TGAAAACCTTGATGGATCTGCTTCTACAGCAGATAATAAACAATCTGACCACCTGTTAATGGTTATTGCATACAATAAGTGGTCTCGCATACTAAGAGAGgtcataaaac ... tcaattgcagAATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGTACAGTGATGTATATGGTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagaaaaaagaacatcagttccaaggttttctaatatgtgattttcaattgcagAATGGAGCTAGATCTGCCCATCAGTTTTGCCGTTCATTCTACTTGAACAGTACAGTGATGTATATGGTCAG
                             ttctaat  putative branch site (score: 7)
                                          ttttc  putative PPT
                                taatatgtgatttt  TA-rich tract