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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacgccttctttttcaaattgaggttgcagacgcttctttgcggaaatgactttgtttaccttggaactgatctttgtaatgtaatgctgtctttttttgcgcgtatgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTGCCACCGAAGCGGCTATCTGGACAGTACCATCCGATCCGGTAAAGTGAGT

Basic information

species Physcomitrella patens
transcript PP1S237_67V6.1
intron # 9
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|208383128|gb|DC919575.1|DC919575
EST:     TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACG                         CTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTA
genomic: TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
EST: gi|18335350|gb|BJ167368.1|BJ167368
EST:     TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACG                         CTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
genomic: TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
EST: gi|37835761|gb|BJ593773.1|BJ593773
EST:     TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACG                         CTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
genomic: TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
EST: gi|162277084|gb|FC453806.1|FC453806
EST:     TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACG                         CTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
genomic: TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
EST: gi|208351084|gb|DC926005.1|DC926005
EST:     TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACG                         CTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
genomic: TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
EST: gi|162220024|gb|FC395370.1|FC395370
EST:     ATCCAATCCTGAATGCTATATACTACACG                         CTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
genomic: ATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
EST: gi|208366076|gb|DC954917.1|DC954917
EST:     TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACG                         CTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
genomic: TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
EST: gi|162249528|gb|FC428098.1|FC428098
EST:     TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACG                         CTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
genomic: TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
EST: gi|208370515|gb|DC952218.1|DC952218
EST:     TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACG                         CTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG
genomic: TTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTG

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), 34 (downstream exon)
Score: 2

ATGACCTTCTCTGTATTCAACAAAGCTATTGACTTGGACGTTCTGTATCATCCAATCCTGAATGCTATATACTACACGgtaagacgcc ... atgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTGCCACCGAAGCGGCTATCTGGACAGTACCATCCGATCCGGTAAAGTGAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggaactgatctttgtaatgtaatgctgtctttttttgcgcgtatgaatgcagCTTGTGGAGATCGTTCCTTCAGCTCTGGTCCTGTATATTTTGCGCAAGTTGCCACCGAAGCGGCTATCTGGACAGTACCATCCGATCCGGTAAAGTGAGT
     aactgat  putative branch site (score: 2)
                 taatgtaat  TA-rich tract