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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtgccatgtttgatcaatgtattttccactgtggtttaagctagcagtaattttcgaactttctcagaaggaggaagtagatcactttcctgtggttatgaacgagttagtcgtaacatgtgcggatcacgttggcaatttctgaaattgtggcttaaaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGACTCATTGGGCTGTGGGCTACTAACGGCCTTATCAAT

Basic information

species Physcomitrella patens
transcript PP1S98_136V6.2
intron # 2
splice site 3'
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|67578663|gb|BJ950830.1|BJ950830
EST:     CGAGACGAGCGCCGCCGNTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: CGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|67578873|gb|BJ951040.1|BJ951040
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162210330|gb|FC386210.1|FC386210
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|67574583|gb|BJ947407.1|BJ947407
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|67701028|gb|BJ961261.1|BJ961261
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162250085|gb|FC427394.1|FC427394
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|67571413|gb|BJ944237.1|BJ944237
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162262839|gb|FC438751.1|FC438751
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162269838|gb|FC445888.1|FC445888
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162250084|gb|FC427393.1|FC427393
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|67700665|gb|BJ960898.1|BJ960898
EST:     ACGAGACGAGCGCCGCCGCTGAGGA-TTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162276312|gb|FC452419.1|FC452419
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|67691902|gb|BJ952135.1|BJ952135
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162223989|gb|FC400347.1|FC400347
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|7583735|gb|AW699641.1|AW699641
EST:     AGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: AGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162226371|gb|FC403287.1|FC403287
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162236290|gb|FC411409.1|FC411409
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|15728457|gb|BI740797.1|BI740797
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|19790227|gb|BQ041763.1|BQ041763
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162261462|gb|FC438298.1|FC438298
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162226370|gb|FC403286.1|FC403286
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|37847166|gb|BJ605174.1|BJ605174
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|67695443|gb|BJ955676.1|BJ955676
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162216551|gb|FC392448.1|FC392448
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162246712|gb|FC424694.1|FC424694
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162269839|gb|FC445889.1|FC445889
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|67694743|gb|BJ954976.1|BJ954976
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|162210329|gb|FC386209.1|FC386209
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
EST: gi|67701356|gb|BJ961589.1|BJ961589
EST:     ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCG                         TGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA
genomic: ACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGA

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), 35 (downstream exon)
Score: 210

TTTGACGATTGTCGCTGCTAAAGCTACCAAGGAGGCTGAGGCCGCCGTGGACGAGACGAGCGCCGCCGCTGAGGATTTTCTCCAGAGCTTGACGGAAGCGgtactgtgcc ... aaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGACTCATTGGGCTGTGGGCTACTAACGGCCTTATCAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacatgtgcggatcacgttggcaatttctgaaattgtggcttaaaattctcagTGGGAGAAGTCGGATGATAAGCCCGCCATTGTTGGACTAGGATTTGCCGGACTCATTGGGCTGTGGGCTACTAACGGCCTTATCAAT
 tcgtaac  putative branch site (score: 210)
                                                ttctc  putative PPT
                                          ttaaaattct  TA-rich tract