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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttccaatcattttttcggacttagtcttgtagggaggagtttttagtttcaatcacgtatgtataactaagttcctcagtgttgttgcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAAAGGCGATGATTGATTTCACCGATCTGTTTTCTGTAATTCATCTGGTGTT

Basic information

species Physcomitrella patens
transcript PP1S83_251V6.1
intron # 1
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|100390663|gb|BY971418.1|BY971418
EST:     TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATG                         TTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
genomic: TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATGgtgtgtgagg ... gcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
EST: gi|18354190|gb|BJ186246.1|BJ186246
EST:     TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATG                         TTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
genomic: TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATGgtgtgtgagg ... gcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
EST: gi|208357963|gb|DC938834.1|DC938834
EST:     TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATG                         TTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
genomic: TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATGgtgtgtgagg ... gcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
EST: gi|18354741|gb|BJ186799.1|BJ186799
EST:     TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATG                         TTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
genomic: TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATGgtgtgtgagg ... gcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
EST: gi|18351529|gb|BJ183581.1|BJ183581
EST:     TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATG                         TTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
genomic: TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATGgtgtgtgagg ... gcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
EST: gi|67717787|gb|BJ968046.1|BJ968046
EST:     TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATG                         TTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
genomic: TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATGgtgtgtgagg ... gcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
EST: gi|18356642|gb|BJ188701.1|BJ188701
EST:     TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATG                         TTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA
genomic: TTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATGgtgtgtgagg ... gcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAA

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: 28 (upstream exon), 26 (downstream exon)
Score: 5

CAGAGCTAAATTCTCCCTACACCGGAGCGCCAGATACTCGTTCGAATAGTTTGGTCGCGTATGATCGCGAGGTTCAAGCGTCGGGGAGGAATTAGCAATGgtgtgtgagg ... gcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAAAGGCGATGATTGATTTCACCGATCTGTTTTCTGTAATTCATCTGGTGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagtttcaatcacgtatgtataactaagttcctcagtgttgttgcttttgcagTTCAACTAGTACACAGTGAATGTGCACAAATTTCACTGTGGAATTCTGGAAAGGCGATGATTGATTTCACCGATCTGTTTTCTGTAATTCATCTGGTGTT
                   gtataac  putative branch site (score: 5)
                                           ttgctttt  putative PPT
                tatgtataa  TA-rich tract