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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGTTGGCATCGTTAAGTTGATGGGAAGGCAGAGTGGATTTATTGCCATGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAGgtagaattcctgtccaatatcgattctgtgctcttttaagcatttcactacaatttcttgttccttgaacagttgacgtggtggcttcctactgtgataa...

Basic information

species Physcomitrella patens
transcript PP1S94_106V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S94_106V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G139360_T06 (Zea mays), 5'ss of exon 6
TGGCGTTGGCATCGTTAAGTTGATGGGAAGGCAGAGTGGATTTATTGCCATGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAGgtagaattcctgtccaatatcgattctgtgctcttttaagcatttcactacaatttcttgttccttg-aacagttgacgtggtggcttcctactgtgataa--------
|||  ||||| | || || || ||||||||    || || |||||||| |||||||| ||  |  ||||||| ||||||||||||||||| ||||||||||||  ||        ||| | | || |    | ||| || |  | |  ||   |||| | |  | || ||    | ||  |  |  | |    |   |||         
TGGTATTGGCTTGGTCAAATTAATGGGAAGAAGCAGCGGGTTTATTGCAATGCACGCTTCCCTTTCAAGTGGGCAGGTCGATGTCTGCTTAATACCTGAGgtaatata-------aatgtagcttttactatgtttaaaac--tgccatatgttttcctctcacatgtaagcactaaca-gaagcttacaagttacaatatgaatgaag
















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|162203812|gb|FC379909.1|FC379909
EST:     TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAG                         GTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
genomic: TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAGgtagaattcc ... aaacctgtagGTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
EST: gi|37852524|gb|BJ610532.1|BJ610532
EST:     TCTGCTTGATACCTGAG                         GTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
genomic: TCTGCTTGATACCTGAGgtagaattcc ... aaacctgtagGTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
EST: gi|7648346|gb|AW739329.1|AW739329
EST:     TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAG                         GTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
genomic: TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAGgtagaattcc ... aaacctgtagGTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
EST: gi|7648257|gb|AW739240.1|AW739240
EST:     TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAG                         GTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
genomic: TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAGgtagaattcc ... aaacctgtagGTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
EST: gi|100428968|gb|BY959524.1|BY959524
EST:     TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAG                         GTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
genomic: TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAGgtagaattcc ... aaacctgtagGTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
EST: gi|162229044|gb|FC404754.1|FC404754
EST:     TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAG                         GTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT
genomic: TGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAGgtagaattcc ... aaacctgtagGTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATAT

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: 35 (upstream exon), 18 (downstream exon)
Score: 6

TGGCGTTGGCATCGTTAAGTTGATGGGAAGGCAGAGTGGATTTATTGCCATGCACGCGTCTTTGGCAAGTGGTCAGGTCGATGTCTGCTTGATACCTGAGgtagaattcc ... aaacctgtagGTAAAATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATATTTACTCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCG




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