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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGATGTCGAAGTGGCCTCCGCGCTCTCCCCCCCTTCATTCTCTCCGGCTGTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgtttcggacctcgtttaatttgttgtttattttatcttttcggcttgttgtggacttgtagttgagatcgttagtgtagtttccgggtagctag...

Basic information

species Physcomitrella patens
transcript PP1S47_244V6.1
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|18374800|gb|BJ206378.1|BJ206378
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18366948|gb|BJ199028.1|BJ199028
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18326122|gb|BJ158121.1|BJ158121
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18374190|gb|BJ205768.1|BJ205768
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|100399062|gb|BY954180.1|BY954180
EST:     GTCACTCGGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18367539|gb|BJ199622.1|BJ199622
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18374946|gb|BJ206524.1|BJ206524
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18329595|gb|BJ161601.1|BJ161601
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTGCTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18329333|gb|BJ161339.1|BJ161339
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18363432|gb|BJ195504.1|BJ195504
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18364334|gb|BJ196407.1|BJ196407
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|100446323|gb|CJ970622.1|CJ970622
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18371365|gb|BJ202967.1|BJ202967
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
EST: gi|18358406|gb|BJ190465.1|BJ190465
EST:     GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAG                         GTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC
genomic: GTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTC

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: 14 (upstream exon), 22 (downstream exon)
Score: 1

CCGATGTCGAAGTGGCCTCCGCGCTCTCCCCCCCTTCATTCTCTCCGGCTGTCACTCCGCTTGACGGGTTCTTTTCACATCCGTCTCCGGATTTGTGTAGgtgtgtgttt ... tgggattcagGTGCTGTGGATGATAGCGGAGTGGTGATAGATCTTTGAGTACTGGAGCTTCGGAGGCTCGAATAGCAGAATGGCAGCCTTTATGGTGGCTGCCGTGGCCG




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