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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCAGATGTGGGGGGTTTTGTAAGCGATCCCGCTGAGGAGCTCGTGGCACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttctgatcgcctcacattgtgtgtggggtgggcatttagggactggaaatagctgtgaggcggtggaagcctcttgaaactaggagcatggag...

Basic information

species Physcomitrella patens
transcript PP1S61_296V6.1
intron # 1
splice site 5'
intron type U2

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|18352881|gb|BJ184936.1|BJ184936
EST:     CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAA                         TATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
genomic: CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttc ... agatgtgcagTATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
EST: gi|67717318|gb|BJ967577.1|BJ967577
EST:     CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAA                         TATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGNTTCTGGGGC
genomic: CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttc ... agatgtgcagTATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
EST: gi|18342506|gb|BJ174541.1|BJ174541
EST:     CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAA                         TATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
genomic: CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttc ... agatgtgcagTATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
EST: gi|67712937|gb|BJ966386.1|BJ966386
EST:     CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAA                         TATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
genomic: CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttc ... agatgtgcagTATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
EST: gi|18347544|gb|BJ179591.1|BJ179591
EST:     CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAA                         TATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
genomic: CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttc ... agatgtgcagTATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
EST: gi|18357166|gb|BJ189225.1|BJ189225
EST:     CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAA                         TATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
genomic: CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttc ... agatgtgcagTATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
EST: gi|18345966|gb|BJ178009.1|BJ178009
EST:     CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAA                         TATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
genomic: CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttc ... agatgtgcagTATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
EST: gi|18352756|gb|BJ184811.1|BJ184811
EST:     CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAA                         TATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC
genomic: CACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttc ... agatgtgcagTATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGC

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: 34 (upstream exon), 28 (downstream exon)
Score: 9

TGCTGCAGATGTGGGGGGTTTTGTAAGCGATCCCGCTGAGGAGCTCGTGGCACCGAGCGAGGCGTTTCGGCAGCGCGCGTTAGTGGCGTCCCGGGCGCAAgtaaggcttc ... agatgtgcagTATGACGAGATGTACAAGCGATCCGTGGAGGATCCCGACGGGTTCTGGGGCGACATCGCATCCACATTCTTTTGGAAGAAAAAATGGCCGACAACAGAAG




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