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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttctcaatctaagttgatatctcacttatttgttgaattctcaattactcaactgcgtgttgacccactgtatctaactgtatttgaaacattcctttgacagcttcttgtgattgttgctccgctcttcttccgccgtaatgcgttctcagtttttctgatagatttcattgtgtgtctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGTGTCATTGTCGACCCAACATGCAGCGACTGCGTAACTTTAGACTATTTAA

Basic information

species Physcomitrella patens
transcript PP1S69_28V6.1
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|208385965|gb|DC956803.1|DC956803
EST:     GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
genomic: GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
EST: gi|162263751|gb|FC440157.1|FC440157
EST:     GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
genomic: GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
EST: gi|7584129|gb|AW700026.1|AW700026
EST:     TCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
genomic: TCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
EST: gi|162233761|gb|FC410027.1|FC410027
EST:     GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
genomic: GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
EST: gi|162187912|gb|FC364486.1|FC364486
EST:     GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAG
genomic: GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAG
EST: gi|162233762|gb|FC410028.1|FC410028
EST:     GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACNAGATAGACGT
genomic: GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
EST: gi|162259504|gb|FC435015.1|FC435015
EST:     GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
genomic: GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
EST: gi|37826256|gb|BJ584268.1|BJ584268
EST:     GAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
genomic: GAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
EST: gi|208378344|gb|DC923015.1|DC923015
EST:     GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
genomic: GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
EST: gi|162187911|gb|FC364485.1|FC364485
EST:     GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
genomic: GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
EST: gi|162265235|gb|FC440158.1|FC440158
EST:     GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAG                         GAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT
genomic: GAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGT

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: 35 (upstream exon), 34 (downstream exon)
Score: 21

GCAATGAGGCTGTTTGTAGGTGAACCTGTCTGGACCCCATATAACCGACCCCAAGATGAACACCCTGTGAGgtgagtttct ... tctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGTGTCATTGTCGACCCAACATGCAGCGACTGCGTAACTTTAGACTATTTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgccgtaatgcgttctcagtttttctgatagatttcattgtgtgtctacttcagGAAGGATTATATCAACAACTTTTTGAAGACCCATTTAGACAAGATAGACGTGTCATTGTCGACCCAACATGCAGCGACTGCGTAACTTTAGACTATTTAA
                       ttctgat  putative branch site (score: 21)
                                             tctacttc  putative PPT
                            atagattt  TA-rich tract