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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAGGACTGATCACATTCTTGCATGCAAGCTTCGACATGAAAACTTTTGTTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctcaatttaattttttgcacagtgactatttcaaacgtaaacgttgcagatagctgcttgtgtaatttcaatatttttctattagattgctccagagattcttgcttatgctggtctttgcatcatgtgtgggtttcactaaaattgttcatttttgcgatgatag

Basic information

species Physcomitrella patens
transcript PP1S414_22V6.1
intron # 23
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|162196692|gb|FC373825.1|FC373825
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162154533|gb|FC330743.1|FC330743
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCANACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162181393|gb|FC358449.1|FC358449
EST:     CAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: CAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|37846088|gb|BJ604096.1|BJ604096
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162275984|gb|FC452052.1|FC452052
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162255375|gb|FC432101.1|FC432101
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162192599|gb|FC370646.1|FC370646
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|37828992|gb|BJ587004.1|BJ587004
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162196103|gb|FC372742.1|FC372742
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162172803|gb|FC348392.1|FC348392
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162192598|gb|FC370645.1|FC370645
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162154532|gb|FC330742.1|FC330742
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|19790154|gb|BQ041724.1|BQ041724
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|37827917|gb|BJ585929.1|BJ585929
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162175300|gb|FC351498.1|FC351498
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|37832308|gb|BJ590320.1|BJ590320
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|162198495|gb|FC375330.1|FC375330
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|37848660|gb|BJ606668.1|BJ606668
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|15327138|gb|BI487641.1|BI487641
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
EST: gi|37824938|gb|BJ583004.1|BJ583004
EST:     TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAG                         CCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT
genomic: TTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCT

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: 25 (upstream exon), 35 (downstream exon)
Score: 14

GGCAGGACTGATCACATTCTTGCATGCAAGCTTCGACATGAAAACTTTTGTTCTTGGCAAATTCCATTACGTTCTCTATTTCCTTGTTCTGGCCATGCAGgtaaaacctc ... gcgatgatagCCTCGGATGCTGATAACTCTAGATGAGAATCTCAAACCTCTACCTGTACCTGTACGAGTCGGCCAAGCTGTTGATGTAGTTGGTCAAGCGGGTCGTCCTA




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