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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAACTATCACTCGGGTTGTCATTGTCCCGAAGGCTTTCAAGGGAACGGATCGGCGGGTGCCGGTGGTTGCGTAGgtgaacattcatattcttccttttatcttagtgtgctgataacacctctgcatcaatccaacctctgaatatggtttgcctcttcgtattgttagacaactatcaaatgtatcgagggattgcagaagaagtgggtggaagcagtagcttaatagagttgctctgggtgcag

Basic information

species Physcomitrella patens
transcript PP1S76_79V6.1
intron # 7
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|37848184|gb|BJ606192.1|BJ606192
EST:     CCCGAAGGCTTTCAAGGGAACGGATCGGCGGGGTGCCGGTGGTTGCGTAG                         ATATCGACGAATGCAAAGAAAAAACCAAATGTCCAGTGCCCTGAAAGTAAA
genomic: CCCGAAGGCTTTCAAGGGAACGGATCGGC-GGGTGCCGGTGGTTGCGTAGgtgaacattc ... ctgggtgcagATATCGACGAATGCAAAGAAAAAACCAAATGT-CAGTGCCCTGAATGTAAA
EST: gi|37853262|gb|BJ611270.1|BJ611270
EST:     TCCCGAAGGCTTTCAAGGGAACGGATCGGCGGGTGCCGGTGGTTGCGTAG                         ATATCGACGAATGCAAAGAAAAAACCAAATGTCAGTGCCCTGAAAGTAAAT
genomic: TCCCGAAGGCTTTCAAGGGAACGGATCGGCGGGTGCCGGTGGTTGCGTAGgtgaacattc ... ctgggtgcagATATCGACGAATGCAAAGAAAAAACCAAATGTCAGTGCCCTGAATGTAAAT
EST: gi|67727112|gb|BJ977371.1|BJ977371
EST:     TCCCGAAGGCTTTCAAGGGAACGGATCGGCGGGTGCCGGTGGTTGCGTAG                         ATATCGACGAATGCAAAGAAAAAACCAAATGTCAGTGCCCTGAATGTAAAT
genomic: TCCCGAAGGCTTTCAAGGGAACGGATCGGCGGGTGCCGGTGGTTGCGTAGgtgaacattc ... ctgggtgcagATATCGACGAATGCAAAGAAAAAACCAAATGTCAGTGCCCTGAATGTAAAT

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: 22 (upstream exon), 22 (downstream exon)
Score: 2

GAGAACTATCACTCGGGTTGTCATTGTCCCGAAGGCTTTCAAGGGAACGGATCGGCGGGTGCCGGTGGTTGCGTAGgtgaacattc ... ctgggtgcagATATCGACGAATGCAAAGAAAAAACCAAATGTCAGTGCCCTGAATGTAAATGTACCAACACATGGGGCTCCTACAACTGCGAATGCTCTGGCGGACTTCT




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