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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtgcacatctcgatcttagactctgattttgccttcaaattatttatgtgttattgcaattagtcaataaagtttcctagacagtttatgatgtttttctttctcgttttttatgtagGCTATGGAGGAGGATCGTGCCAGTGTACAAATCGAACAGATTCCGCTTGAAAAGTGTGACGAACGCCTCAGTGATCAGTAACATCATGTTGACGGATTGA

Basic information

species Physcomitrella patens
transcript PP1S45_55V6.1
intron # 5
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|162175626|gb|FC351824.1|FC351824
EST:     TAGCAGTCAGTCAAGTGGGAATCCCAAATTTTACACACACTCAACTTCAG                         GCTATGGAGGAGGATCGTGCCAGTGTACAAATCGAACAGATTCCGCTTGAA
genomic: TAGCAGTCAGTCAAGTGGGAATCCCAAATTTTACACACACTCAACTTCAGgtactgtgca ... ttttatgtagGCTATGGAGGAGGATCGTGCCAGTGTACAAATCGAACAGATTCCGCTTGAA
EST: gi|67695210|gb|BJ955443.1|BJ955443
EST:     TAGCAGTCAGTCAAGTGGGAATCCCAAATTTTACACACACTCAACTTCAG                         GCTATGNAGGAGGATCGTGCCAGTGTACAAATCGAACAGATTCCGCTTGAA
genomic: TAGCAGTCAGTCAAGTGGGAATCCCAAATTTTACACACACTCAACTTCAGgtactgtgca ... ttttatgtagGCTATGGAGGAGGATCGTGCCAGTGTACAAATCGAACAGATTCCGCTTGAA
EST: gi|67697779|gb|BJ958012.1|BJ958012
EST:     TAGCAGTCAGTCAAGTGGGAATCCCAAATTTTACACACACTCAACTTCAG                         GCTATGGAGGAGGATCGTGCCAGTGTACAAATCGAACAGATTCCGCTTGAA
genomic: TAGCAGTCAGTCAAGTGGGAATCCCAAATTTTACACACACTCAACTTCAGgtactgtgca ... ttttatgtagGCTATGGAGGAGGATCGTGCCAGTGTACAAATCGAACAGATTCCGCTTGAA

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-Seq library.


Block sizes: 9 (upstream exon), 27 (downstream exon)
Score: 1

GGGTCTTCCTGTTGAACAGGCAGTTTTAATGGGTAACTATTTTGGAGGTTTAGCAGTCAGTCAAGTGGGAATCCCAAATTTTACACACACTCAACTTCAGgtactgtgca ... ttttatgtagGCTATGGAGGAGGATCGTGCCAGTGTACAAATCGAACAGATTCCGCTTGAAAAGTGTGACGAACGCCTCAGTGATCAGTAACATCATGTTGACGGATTGA































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaataaagtttcctagacagtttatgatgtttttctttctcgttttttatgtagGCTATGGAGGAGGATCGTGCCAGTGTACAAATCGAACAGATTCCGCTTGAAAAGTGTGACGAACGCCTCAGTGATCAGTAACATCATGTTGACGGATTGA
                            tgtttttctttctcgt  CT-rich tract
                     tttatgatgttttt  TA-rich tract