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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTGGGTGGGTCGTCGGCTTTGAAAGCCAGCTCGGTGTTCAATTCGGCCTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttctcaatcctactcagaatgagcaactctggaatctgaagttcacattcgattggtgctactggaaattcttgctaataggccagagttagga...

Basic information

species Physcomitrella patens
transcript PP1S93_67V6.2
intron # 1
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|208359165|gb|DC934668.1|DC934668
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... tttgcatcagGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
EST: gi|208364545|gb|DC930935.1|DC930935
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... tttgcatcagGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
EST: gi|100387906|gb|BY970651.1|BY970651
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... tttgcatcagGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
EST: gi|208387152|gb|DC945451.1|DC945451
EST:     TCACATNTCCCGTGG                         GTGAGGCGAGAGA-GGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
genomic: TCACATGTCCCGTGGgtgggtttct ... tttgcatcagGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
EST: gi|67572936|gb|BJ945760.1|BJ945760
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... tttgcatcagGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
EST: gi|100426838|gb|BY977388.1|BY977388
EST:     CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGG                         GTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG
genomic: CTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... tttgcatcagGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGG

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: 29 (upstream exon), 35 (downstream exon)
Score: 12

TGGTTGGGTGGGTCGTCGGCTTTGAAAGCCAGCTCGGTGTTCAATTCGGCCTCTTCGTCGTTTCAAGGCCGGATTTGTCTGTTTCTCACATGTCCCGTGGgtgggtttct ... tttgcatcagGTGAGGCGAGAGAGGGTAGAAGGGTAGGAGTTCAAGCGTCTTTGCTTGGGGTAGGCGCCCCGGAAGCTTTGGTGATAGGCGTGGTGGCACTGCTCGTGTT




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