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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcgtctaagcttcagccacagaaaatcacagaagcaagatgatcatacattttctttccttttctttttttttttgaattcttgtttcttctgaaccagAACAATGAGCAGGTTGTTCAACAGCAATGAACACTTCCCATGCGAAGGAACGGGATCTTCCACAGTTCCAAGTACTCGTGAATCAGATCTCTTTAGACTA

Basic information

species Physcomitrella patens
transcript PP1S77_21V6.2
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|15327381|gb|BI488009.1|BI488009
EST:     GCCTCCAAGCCATGGCGAGGAAGGCTGGTATCAATCTGGCTGACTACTAG                         AACAATGAGCAGGTTGTTCAACAGCAATGAACACTTCCCATGCGAAGGAAC
genomic: GCCTCCAAGCCATGGCGAGGAAGGCTGGTATCAATCTGGCTGACTACTAGgtcagtgccg ... tctgaaccagAACAATGAGCAGGTTGTTCAACAGCAATGAACACTTCCCATGCGAAGGAAC




















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: 22 (upstream exon), 23 (downstream exon)
Score: 4

CGTGAAGCTCCGCATTTCAACCAAGGCGCTGAAGACGATCGAGAAGAACGGCCTCCAAGCCATGGCGAGGAAGGCTGGTATCAATCTGGCTGACTACTAGgtcagtgccg ... tctgaaccagAACAATGAGCAGGTTGTTCAACAGCAATGAACACTTCCCATGCGAAGGAACGGGATCTTCCACAGTTCCAAGTACTCGTGAATCAGATCTCTTTAGACTA































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacattttctttccttttctttttttttttgaattcttgtttcttctgaaccagAACAATGAGCAGGTTGTTCAACAGCAATGAACACTTCCCATGCGAAGGAACGGGATCTTCCACAGTTCCAAGTACTCGTGAATCAGATCTCTTTAGACTA
       ttctttccttttcttt  CT-rich tract
               ttttcttttttttttt  TA-rich tract