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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTACCGAAGAACATCATCAACGCTGACATCGTCTTGACCGGCGTCTCCCGCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAAgtgaattccctttctctaaacacacccttccatattgattccccctttaccaaactctaatcttgtgaattttacaaatcagtgcctgtcgaatcggttctttgagactcaactctctgcaactctgtacag

Basic information

species Physcomitrella patens
transcript PP1S123_99V6.1
intron # 3
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|208356171|gb|DC918411.1|DC918411
EST:     GCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAA                         GTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
genomic: GCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAAgtgaattccc ... ctctgtacagGTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
EST: gi|67697862|gb|BJ958095.1|BJ958095
EST:     GCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAA                         GTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
genomic: GCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAAgtgaattccc ... ctctgtacagGTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
EST: gi|208355342|gb|DC949836.1|DC949836
EST:     CAGCAAAACGNCTCTCTCCACATACATGGCGCAAAAGGGTTACAAA                         GTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
genomic: CAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAAgtgaattccc ... ctctgtacagGTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
EST: gi|162180587|gb|FC356944.1|FC356944
EST:     GCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAA                         GTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
genomic: GCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAAgtgaattccc ... ctctgtacagGTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
EST: gi|37851332|gb|BJ609340.1|BJ609340
EST:     CCACATACATGGCGCAAAAGGGTTACAAA                         GTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
genomic: CCACATACATGGCGCAAAAGGGTTACAAAgtgaattccc ... ctctgtacagGTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
EST: gi|37842891|gb|BJ600899.1|BJ600899
EST:     CACCAGCAAAACGCCTCTNTCCCACATACATGGCGCAAAAGGGTTACAAA                         GTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
genomic: CACCAGCAAAACGCCTCTCT-CCACATACATGGCGCAAAAGGGTTACAAAgtgaattccc ... ctctgtacagGTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
EST: gi|208361876|gb|DC953926.1|DC953926
EST:     GCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAA                         GTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC
genomic: GCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAAgtgaattccc ... ctctgtacagGTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTC

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: 31 (upstream exon), 34 (downstream exon)
Score: 12

ATTACCGAAGAACATCATCAACGCTGACATCGTCTTGACCGGCGTCTCCCGCACCAGCAAAACGCCTCTCTCCACATACATGGCGCAAAAGGGTTACAAAgtgaattccc ... ctctgtacagGTCGCGAATGTGCCTCTGGTGCTGGGCATCGATCCGCCCAAGGAACTCTTCGAGGTGGATCAGGACAAGGTTTTCGGCTTGACCATCAATCCGAGCTATC




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