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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCAAATGACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgtttttctctcttgtctgtcttctttttaatatatcaatcaaattatactagcaagtatgtaagggtgagttcttcgaaagttatcgcgagctagcaatattttgactacctgggtttatttatgttgccag

Basic information

species Physcomitrella patens
transcript PP1S39_248V6.1
intron # 5
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:     ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGA                         CTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAA-
genomic: ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
EST: gi|100441417|gb|BY962706.1|BY962706
EST:     ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGA                         CTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
genomic: ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
EST: gi|100360990|gb|BY946858.1|BY946858
EST:     ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGA                         CTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
genomic: ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
EST: gi|208347324|gb|DC909715.1|DC909715
EST:     ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGA                         CTTGCCATGCGTGAGGTGTGCAAATATATCGATGACAAGCTTGCTACAAAA
genomic: ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
EST: gi|100417876|gb|BY993228.1|BY993228
EST:     ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGA                         CTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
genomic: ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
EST: gi|208360034|gb|DC934923.1|DC934923
EST:     ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGA                         CTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
genomic: ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
EST: gi|100449912|gb|CJ973999.1|CJ973999
EST:     ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGA                         CTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
genomic: ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
EST: gi|18373059|gb|BJ204661.1|BJ204661
EST:     ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGA                         CTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
genomic: ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
EST: gi|67719559|gb|BJ969818.1|BJ969818
EST:     ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGA                         CTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA
genomic: ACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA

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: 23 (upstream exon), 13 (downstream exon)
Score: 1

AGAGCAAATGACTTAGTTAGGATCAAGATACATCCCACTTCAATCATTAGTGGTTATCGAgtaagtttgt ... atgttgccagCTTGCCATGCGTGAGGCGTGCAAATATATCGATGACAAGCTTGCTACAAAA




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