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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttagtcaattcctatgattcagtagactaccggaaatctggtcaatttttttataatcacttgacctgctcatttgataggactggtctctgaatttatctcgtttcgaaggtttcttctttttcttcttctaattattattattattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTCGGTGCATATGTACTAGG

Basic information

species Physcomitrella patens
transcript PP1S6_302V6.1
intron # 4
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|208388113|gb|DC941724.1|DC941724
EST:     CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAG                         GTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
genomic: CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAGgtgttagtca ... tattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
EST: gi|100444725|gb|BY982554.1|BY982554
EST:     CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAG                         GTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
genomic: CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAGgtgttagtca ... tattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
EST: gi|208380026|gb|DC914576.1|DC914576
EST:     CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAG                         GTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
genomic: CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAGgtgttagtca ... tattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
EST: gi|208364237|gb|DC935508.1|DC935508
EST:     TACGCCCTTCGATGCGATGCAG                         GTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
genomic: TACGCCCTTCGATGCGATGCAGgtgttagtca ... tattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
EST: gi|100426269|gb|BY958812.1|BY958812
EST:     CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAG                         GTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
genomic: CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAGgtgttagtca ... tattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
EST: gi|100434101|gb|BY978959.1|BY978959
EST:     CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAG                         GTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
genomic: CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAGgtgttagtca ... tattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
EST: gi|100417753|gb|BY975636.1|BY975636
EST:     CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAG                         GTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC
genomic: CTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAGgtgttagtca ... tattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTC

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: 26 (upstream exon), 20 (downstream exon)
Score: 5

AAGTGGGAGCTTGGGAATCTGTTCAAGCTGCAATGCCTACGCCCTTCGATGCGATGCAGgtgttagtca ... tattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTCGGTGCATATGTACTAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtttcgaaggtttcttctttttcttcttctaattattattattattttccagGTTTGGGATTACGAAGGGCTTGGGTACACTCGTTACACTGCTGACGACGTCGGTGCATATGTACTAGG
                             ttctaat  putative branch site (score: 5)
                                            ttattttcc  putative PPT
             tttcttctttttcttc  TA-rich tract