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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtgttcctgttgatcgactccgttgtattttgtagatgtagatcgcgagcacctgtttattgcaacttcttgattcaatcatttcaaaactgctgttgttcctatgtgcgggtttttgatttttatatatttgcaatttcttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGCCACACATTCAACAACTGGGTGTTCATTCTCGTCCTCACTTTCACAGTTG

Basic information

species Physcomitrella patens
transcript PP1S37_351V6.1
intron # 8
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|162212511|gb|FC388487.1|FC388487
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|37851230|gb|BJ609238.1|BJ609238
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|162255099|gb|FC430714.1|FC430714
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|162174301|gb|FC350684.1|FC350684
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|37829382|gb|BJ587394.1|BJ587394
EST:     ACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: ACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|37853461|gb|BJ611469.1|BJ611469
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|162174302|gb|FC350685.1|FC350685
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|37851341|gb|BJ609349.1|BJ609349
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|162178342|gb|FC355164.1|FC355164
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|162178343|gb|FC355165.1|FC355165
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|162212510|gb|FC388486.1|FC388486
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
EST: gi|208359668|gb|DC930272.1|DC930272
EST:     CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAG                         GTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC
genomic: CCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGC

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), 27 (downstream exon)
Score: 5

GGTGCTGCAGTATAGAGGAAAAGGGTTTTTCCACCTCGAGGGAGAAGACTCCACAATCATATTGAACACAATGATTTTTAATGCGTTTGTTTTCTGTCAGgtactgtgtt ... cttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGCCACACATTCAACAACTGGGTGTTCATTCTCGTCCTCACTTTCACAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttcctatgtgcgggtttttgatttttatatatttgcaatttcttattccagGTATTCAACGAGATCAACTCGCGAGAGATGGGAAAGCTGAATATCTTCCGCCACACATTCAACAACTGGGTGTTCATTCTCGTCCTCACTTTCACAGTTG
                   ttttgat  putative branch site (score: 5)
                                          tttcttattcc  putative PPT
                  tttttgatttttatat  TA-rich tract