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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaacttatttgggtgagtggggaggtcgcgataggtcttgtgcaggccatatctgggttcgcgagcttcacctcatgttcacgtttggttcattttcagGCACTGGCGAGTGAGTATGCGGGGACGGTAATATGTCTGTGGGATTTTCTCTCCGCAGACCAGGTGATTGCCTGTGACTACTCCGGCGCATCCTGAT

Basic information

species Physcomitrella patens
transcript PP1S4_66V6.2
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|18343344|gb|BJ175382.1|BJ175382
EST:     CCGGACGCGGGGGCAGATGTCCTTGGATGATGCCTGGAGGANNNNNNNNG                         GCACTGGCGAGTGAGTATGCGGGGACGGTAATATGTCTGTGGGATTTTCTC
genomic: CCGGACGCGGGGGCAGATGTCCTTGGATGATGCCTGGAGGATTTTTTTTGgtgagggaat ... tcattttcagGCACTGGCGAGTGAGTATGCGGGGACGGTAATATGTCTGTGGGATTTTCTC
EST: gi|100361461|gb|BY984100.1|BY984100
EST:     CCGGACGCGGGGGCAGATGTCCTTGGATGATGCCTGGAGGANNNNNNNNG                         GCACTGGCGAGTGAGTATGCGGGGACGGTAATATGTCTGTGGGATTTTCTC
genomic: CCGGACGCGGGGGCAGATGTCCTTGGATGATGCCTGGAGGATTTTTTTTGgtgagggaat ... tcattttcagGCACTGGCGAGTGAGTATGCGGGGACGGTAATATGTCTGTGGGATTTTCTC

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: 11 (upstream exon), 26 (downstream exon)
Score: 2

TGTGGATGTGGATGTGAATGCGCGCTGTGGCTCCATGTAGGATTTGAGCGCCGGACGCGGGGGCAGATGTCCTTGGATGATGCCTGGAGGATTTTTTTTGgtgagggaat ... tcattttcagGCACTGGCGAGTGAGTATGCGGGGACGGTAATATGTCTGTGGGATTTTCTCTCCGCAGACCAGGTGATTGCCTGTGACTACTCCGGCGCATCCTGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggccatatctgggttcgcgagcttcacctcatgttcacgtttggttcattttcagGCACTGGCGAGTGAGTATGCGGGGACGGTAATATGTCTGTGGGATTTTCTCTCCGCAGACCAGGTGATTGCCTGTGACTACTCCGGCGCATCCTGAT
                                            ttcattttc  CT-rich tract
                                            ttcatttt  TA-rich tract