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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgagtttctcatgcacgaaacctaatggcttagcttttttggccacaattttaatttattgaaattcatgtctatttgatccagtgtggtaaagttccatccaaatgtctgacacacagttgaatggtacattgcattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTGCGAGCGTTGGTCGATCCTGAGGGGGCTATGCGTGATATCCGGGACTTGG

Basic information

species Physcomitrella patens
transcript PP1S277_10V6.3
intron # 5
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|162192890|gb|FC369884.1|FC369884
EST:     GCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162165520|gb|FC340631.1|FC340631
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162155413|gb|FC332027.1|FC332027
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|18327722|gb|BJ159725.1|BJ159725
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|100396902|gb|BY953885.1|BY953885
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAACTTGAA                         CTTTTTGACAAGGC
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGC
EST: gi|208399548|gb|DC908545.1|DC908545
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTANTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162151154|gb|FC327153.1|FC327153
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162198693|gb|FC373474.1|FC373474
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|100367017|gb|BY948326.1|BY948326
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CTTTTTTGACANG-CNGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGT
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTT-GACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGT
EST: gi|162167140|gb|FC343616.1|FC343616
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162159709|gb|FC336095.1|FC336095
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162167477|gb|FC344194.1|FC344194
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|208349541|gb|DC905651.1|DC905651
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTNGTCACCACAAATCANCTTGAA                         CNTTT-GACAAGGCG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCG
EST: gi|162230035|gb|FC405975.1|FC405975
EST:     CCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: CCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162168664|gb|FC343926.1|FC343926
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162170376|gb|FC346781.1|FC346781
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162176795|gb|FC352809.1|FC352809
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162267926|gb|FC444007.1|FC444007
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
EST: gi|162166539|gb|FC343236.1|FC343236
EST:     GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAA                         CCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG
genomic: GAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTG

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), 33 (downstream exon)
Score: 23

AGTTGGACTTCAGATTTCCAGTGGGAGCACCTCTGCACGGCATAAAAGCGTTTGTCACCACAAATCAGCTTGAAgtaagtcgag ... cattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTGCGAGCGTTGGTCGATCCTGAGGGGGCTATGCGTGATATCCGGGACTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaagttccatccaaatgtctgacacacagttgaatggtacattgcattttacagCCTTTTGACAAGGCGGCGAACGCAGTGGCATTGGCAACTAGTCCAGTTGTGCGAGCGTTGGTCGATCCTGAGGGGGCTATGCGTGATATCCGGGACTTGG
                 gtctgac  putative branch site (score: 23)
                                              attttaca  TA-rich tract