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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggggccgccgacagcgcgagtcggtgtcgtgtgagggggcatgaggacggctgacatgggtggtggcgctgacacgcgaaattttgatgggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGAGACGGGGGCGGGGAAGCACGTCCCGCGCGCCGTGTTCGTGGATCTGGAG

Basic information

species Physcomitrella patens
transcript PP1S341_23V6.2
intron # 2
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|18324871|gb|BJ156866.1|BJ156866
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162167933|gb|FC344871.1|FC344871
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|18358529|gb|BJ190588.1|BJ190588
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|100420027|gb|BY975938.1|BY975938
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|18331875|gb|BJ163887.1|BJ163887
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162153183|gb|FC329589.1|FC329589
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162197748|gb|FC374998.1|FC374998
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162229157|gb|FC404516.1|FC404516
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162186501|gb|FC363265.1|FC363265
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162159253|gb|FC335106.1|FC335106
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162174343|gb|FC350414.1|FC350414
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|18353132|gb|BJ185187.1|BJ185187
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|18366573|gb|BJ198652.1|BJ198652
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162162283|gb|FC338065.1|FC338065
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
EST: gi|162195647|gb|FC370310.1|FC370310
EST:     GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAG                         CGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA
genomic: GAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGA

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), 35 (downstream exon)
Score: 68

TCAGCATCCACATAGGCCAGGCCGGTATTCAGGTCGGGAATGCGTGCTGGGAGCTGTACTGTCTGGAGCATGGGATTCAGCCCGATGGTCGCATGCCAAGgtacgtggat ... gggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGAGACGGGGGCGGGGAAGCACGTCCCGCGCGCCGTGTTCGTGGATCTGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggacggctgacatgggtggtggcgctgacacgcgaaattttgatgggtttgcagCGACACGACGGTAGGAGGTGGCGACGATGCGTTCAACACATTTTTTAGCGAGACGGGGGCGGGGAAGCACGTCCCGCGCGCCGTGTTCGTGGATCTGGAG
                                   aaattttgat  TA-rich tract