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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actctgttaggggttataatatacttaacctccgaagtaccacatttcctatatcttagctaacccaggcagcttctctgtgttgctttgttgggtgaagGGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCCGCACTGGAAATGGCATTGCTGGTTATTCGCTCCAATCCTACAGTACTTG

Basic information

species Physcomitrella patens
transcript PP1S10_296V6.2
intron # 14
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|37835129|gb|BJ593141.1|BJ593141
EST:     GAGGAGGCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAG                         GGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC
genomic: GAGGAGGCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAGgtaatttcta ... ttgggtgaagGGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC
EST: gi|162165055|gb|FC341102.1|FC341102
EST:     AGGAGGCCTTGATGATACTGGTAGTTCCTTCTCCTGNGGGCAA-GATCAG                         GGTCATATGGCGGACATGGTACAAAA
genomic: AGGAGGCCTTGATGATACTGGTAGTTCCTTCTCCTG-GGGCAAAGATCAGgtaatttcta ... ttgggtgaagGGTCATATGGCGGACATGGTACAAAA
EST: gi|18336101|gb|BJ168123.1|BJ168123
EST:     GCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAG                         GGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC
genomic: GCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAGgtaatttcta ... ttgggtgaagGGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC
EST: gi|162173107|gb|FC348693.1|FC348693
EST:     GAGGAGGCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAG                         GGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC
genomic: GAGGAGGCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAGgtaatttcta ... ttgggtgaagGGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC
EST: gi|15320044|gb|BI487478.1|BI487478
EST:     GAGGAGGCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAG                         GGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC
genomic: GAGGAGGCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAGgtaatttcta ... ttgggtgaagGGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC
EST: gi|18339664|gb|BJ171691.1|BJ171691
EST:     GCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAG                         GGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC
genomic: GCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAGgtaatttcta ... ttgggtgaagGGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCC

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), 35 (downstream exon)
Score: 34

GTATGGTCTCAGTCCCATTATTGGTCCGATTTCGTTAGCTACTCTATCTGGAGGAGGCCTTGATGATACTGGTAGTTCCTTCTCCTGGGGCAAAGATCAGgtaatttcta ... ttgggtgaagGGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCCGCACTGGAAATGGCATTGCTGGTTATTCGCTCCAATCCTACAGTACTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctatatcttagctaacccaggcagcttctctgtgttgctttgttgggtgaagGGTCATATGGCGGACATGGTACAAAAAGAGGTGAGATCTTTAATGAACTCCGCACTGGAAATGGCATTGCTGGTTATTCGCTCCAATCCTACAGTACTTG
            agctaac  putative branch site (score: 34)
                                        ctttgtt  putative PPT
     atatctta  TA-rich tract