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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGGCTTGTCAAGCCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgtttttgtgctttactctgtattctactaggtgatacaaggatctattgatgtatatctcagttcgattgatatgtctttcttagtctggtttt...

Basic information

species Physcomitrella patens
transcript PP1S39_248V6.1
intron # 2
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|100450985|gb|CJ974539.1|CJ974539
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|100441417|gb|BY962706.1|BY962706
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|100360990|gb|BY946858.1|BY946858
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|208347324|gb|DC909715.1|DC909715
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|100417876|gb|BY993228.1|BY993228
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|18358450|gb|BJ190509.1|BJ190509
EST:     CCATCGCCAACATTGTGAAAACTTCGNTAGGGC-AGNTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|208360034|gb|DC934923.1|DC934923
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|100449912|gb|CJ973999.1|CJ973999
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|18373059|gb|BJ204661.1|BJ204661
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGG-CAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
EST: gi|67719559|gb|BJ969818.1|BJ969818
EST:     CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAG                         ATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC
genomic: CCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACC

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: 9 (upstream exon), 27 (downstream exon)
Score: 1

TTATGGCTTGTCAAGCCATCGCCAACATTGTGAAAACTTCGTTAGGGCCAGTTGGTCTCGACAAGgttcgtgttt ... tggattacagATGCTTGTGGATGATATCGGCGACGTTACTATAACAAATGATGGAGCTACCATTTTAAAAATGCTTGAGGTGGAGCACCCCGCTGCTAAG




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