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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATGCCGCAACAAGGTTGACAAAGAGAAGTTGATGGCTGGTACTCGAGTTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgtttgtttgattatccggagtgatccctacattctgaagtatagggttaatagcatcgttaacggcgatttggttctggtattgaagtattg...

Basic information

species Physcomitrella patens
transcript PP1S91_182V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S91_182V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G074037_T01 (Zea mays), 5'ss of exon 3
TGGATGCCGCAACAAGGTTGACAAAGAGAAGTTGATGGCTGGTACTCGAGTTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgg--gtttgtt-tgtttgattatccgga-gtgatccctacattctga--agtatagggttaatagcatcgttaacggcgatttggttctggtattgaagtattg
||  ||||| |  || ||||||||||| |||||||| |||||||| |||||||   | || ||||| || || || ||||||||    || ||  | |||||    |||||||   | | ||| | |  | ||| ||    |  | |||  | | | |   | | ||| ||  | |  || || |  ||      ||  ||||   
TGCCTGCCGAAGTAAAGTTGACAAAGAAAAGTTGATTGCTGGTACACGAGTTGTTCTTGACATGACAACACTTACCATTATGCGCATTCTGCCACGTGAGgtatatgtttgttacatattattctgcttatgtgttcgtgtccatttgattacttttgaaatta-agcctctgtgatcgctatctatttacaaactt--agta---
















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|67572554|gb|BJ945378.1|BJ945378
EST:     TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
EST: gi|100386933|gb|BY988202.1|BY988202
EST:     TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
EST: gi|100449435|gb|CJ973734.1|CJ973734
EST:     TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
EST: gi|100448214|gb|CJ972513.1|CJ972513
EST:     TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
EST: gi|67508474|gb|BJ941340.1|BJ941340
EST:     TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
EST: gi|100378570|gb|BY968666.1|BY968666
EST:     TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
EST: gi|100426731|gb|BY977333.1|BY977333
EST:     TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
EST: gi|100403562|gb|BY954988.1|BY954988
EST:     TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
EST: gi|100442911|gb|BY963406.1|BY963406
EST:     TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGC
EST: gi|67703931|gb|BJ964164.1|BJ964164
EST:     TTGCATTGGATATGACTACTCTCACGATTATACGAGCACTTCCCAGAGAG                         GTTGATCCCGTTGTGTACAATATGCTGCACG
genomic: TTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACG

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: 29 (upstream exon), 16 (downstream exon)
Score: 5

TGGATGCCGCAACAAGGTTGACAAAGAGAAGTTGATGGCTGGTACTCGAGTTGCATTGGATATGACTACTCTCACGATTATGCGAGCACTTCCCAGAGAGgtgggtttgt ... attgtgttagGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGCTACTCAGCCGTTGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGT




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