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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatcatgagccttgcgacacctgtctttgtttaatggagtatcgttatttcctttcacatggacactgctaatcattagttaagcttttccatatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCC

Basic information

species Oryza sativa
transcript LOC_Os06g46310.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G069198_T04 (Zea mays), 3'ss of exon 5
-----------------gtcagtatcatgagccttgcgacacctgtctttgtttaatgg-agtatcgttatttcctt-tcacatggacactgctaatcattagttaagcttttccatatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCC
                 || | | |  ||   | | | |  | |  || ||   | ||  | ||     |   |     |   ||  || |||||||  || || ||  |  ||  | | | |||||| || || || ||||||||||| ||||| ||||| ||||  ||||||||  | |||||||||||||| ||||| ||||| |||||||| ||||||||
gttggtattttatgtttgttaatttattgcatccttcaatccttccctgtgagcattgctaatacaacaacaacaaagccttgtgagcattgctaatagtttgtgaaattcctctgtgt-acagGGAAACATCTTGCAGAGCATTGCAGGGCTGAGTATCCCAAGGTCACAAATTTTGTCTTATGGATTCTTGCAGAACTTGCTGTTGTTGCATGTGACATTCC

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 5
gtcagtatcatgagccttgcgacacctgtctttgtttaatggagtatcgttatttcctttcacatggacactgctaatcattagttaagcttttccatatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCC
                 || ||   || | |     || |    | |   ||| | ||  ||  |      | || |||   |     | || |  ||    |||| |||||  | || ||||| ||||||  ||||||||||||||   | || |||||  ||||| ||||||| ||| | |||||||||||||| ||||||||
--------------gtatgtgatttctttatccagctattttcat-tgaatatcttctcccaatttattgatcctcatctccaacgttgtttcttaat--tgtagGAAAGCATTTAGCAGAGCACTGCAGAATTGAATATCCAAAGGTGCCTAACTTCATCCTATGGGTTCTTGCTGAAATTGCTGTAGTTGCATGTGACATTCC
















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|33653430|gb|CF276044.1|CF276044
EST:     TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTG                         GGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATT
genomic: TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTGgtcagtatca ... catatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATT
EST: gi|88692251|gb|CI735826.1|CI735826
EST:     TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTG                         GGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATC
genomic: TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTGgtcagtatca ... catatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATC
EST: gi|44677020|gb|CR290454.1|CR290454
EST:     TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCCAGACTG                         GGAAGCACCTGACCGAGCATTGCAGAGC
genomic: TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTGgtcagtatca ... catatgatagGGAAGCACCTGGCCGAGCATTGCAGAGC
EST: gi|29664628|gb|CB660903.1|CB660903
EST:     TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTG                         GGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATT
genomic: TGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTGgtcagtatca ... catatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATT

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: 54 (upstream exon), 75 (downstream exon)
Score: 26

CTTCTTTGGATCATACTTATTGCGTCATGTGCTGCTCTTATAATTCAATCACTTGCAGCTAGGCTAGGAGTCGTGACTGgtcagtatca ... catatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcctttcacatggacactgctaatcattagttaagcttttccatatgatagGGAAGCACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCC
                     tgctaat  putative branch site (score: 26)
                                       cttttccat  putative PPT
                        taatcattagttaa  TA-rich tract