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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattccttctcttgcactgattattctacttcatatttttcattatgttgcactcagaaagaagctaattgttagcatcttttacattgccaagCTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAAAAGCAGCGAACACAGCGTAGCTATGACTTCACTGGAGTTACATCATGGT

Basic information

species Oryza sativa
transcript LOC_Os04g57350.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G065012_T02 (Zea mays), 3'ss of exon 11
gtatattccttctcttgcactgattattctacttcatatttttcattatgttgcactcagaaagaagctaattgttagcatcttttacattgccaagCTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAAAAGCAGCGAACACAGCGTAGCTATGACTTCACTGGAGTTACATCATGGT
            |      || | |     ||    ||||| ||||   |     ||     |||| ||||     | ||  || |   |    |||||  | || ||  | ||||| ||||||||||| ||||||||||||||||| |||||||| || ||||| ||||| || ||||| ||||| || || ||||
-----------gtacaatccttaatcccacacccagtatttatcatc-cgacttgctgttggagaaactaac-accaccagtttctttgtga--aagCTGTTAGAGCACGTGACCTTCGTGGACACTCCAGGAGTTTTATCAGGGGAGAAGCAGCGGACGCAGCGCAGCTACGATTTCACCGGAGTCACGTCGTGGT

upper sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 11
gtatattccttc-tcttgcactgattattctacttcatatttttcattatgttgcactcagaaagaagctaattgttagcatcttttacattgcc-aagCTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAAAAGCAGCGAACACAGCGTAGCTATGACTTCACTGGAGTTACATCATGGT
|||| ||       ||    ||  | |    |  || |   || | ||    || | | |    |  | ||||||||      ||   | |||   ||||| ||||| ||| |||| ||||| ||||| ||||||||||||||||||||||| ||  ||||||||||    ||||| |||||||| |||||||||||||
gtatgtttaacaacctcatgcttctgacaggagatcgttcattacttttgcctgtattgattt-gctgataattgttgatccattcatctttgtttaagCTGCTGGAGCATGTAACATTTGTCGACACCCCTGGAGTTTTATCAGGGGAAAAACAAAGAACACAGCGAGCATATGATTTCACTGGTGTTACATCATGGT

upper sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 11
gtatattccttctcttgcactgattattctacttcatatttt-tcattatgttgcactcagaaagaagctaattgttagcatcttttacattgccaa-gCTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAAAAGCAGCGAACACAGCGTAGCTATGACTTCACTGGAGTTACATCATGGT
||   ||  | ||||   | | || ||   | ||  ||  || ||||| ||| ||||       ||| || |        |||||||| ||   ||| ||||||||| || || || |||||||| |||||||||||| ||||||| |||||||| |||||||||||   ||| || || ||||| || ||||||||||
gtgagttattactct-ataattatcatggaaatttctagattatcattctgtagcacct-----gaaactta--------atcttttatatgatcaaagCTACTGGAGCACATCACGTTTGTGGATACTCCTGGAGTTCTATCAGGAGAAAAGCAACGAACACAGCGAGCCTACGATTTTACTGGTGTAACATCATGGT

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|3761603|gb|C98851.1|C98851
EST:     TTGGGACAGCATTTCTATCAAAGTTTGAATGTTCTCAGATGCCTCATCCA                         CTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAA
genomic: TTGGGACAGCATTTCTATCAAAGTTTGAATGTTCTCAGATGCCTCATCCAgtatattcct ... cattgccaagCTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAA




















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: 69 (upstream exon), 74 (downstream exon)
Score: 89

AAACACAATTGCCGTGCAAGCAGACATGCCATATAGTGGCTTGTCATCTTTTGGGACAGCATTTCTATCAAAGTTTGAATGTTCTCAGATGCCTCATCCAgtatattcct ... cattgccaagCTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAAAAGCAGCGAACACAGCGTAGCTATGACTTCACTGGAGTTACATCATGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattatgttgcactcagaaagaagctaattgttagcatcttttacattgccaagCTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAAAAGCAGCGAACACAGCGTAGCTATGACTTCACTGGAGTTACATCATGGT
                       agctaat  putative branch site (score: 89)
                                      tcttttac  putative PPT
                          taattgtta  TA-rich tract