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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctctcgtgatggtctaagcctagaaatgttactagacaacaacgtgatattcatgagagcttgacatttccaagccctagtcaataattcattccttcgctggtcgtcaatcatcgactttgttgtgtaaactcattggcttcgatttttgtcttcgtcttgttcacatttttctttctggcagGATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTTGTG

Basic information

species Physcomitrella patens
transcript PP1S336_18V6.2
intron # 9
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|162275556|gb|FC451298.1|FC451298
EST:     ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTG                         GATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
genomic: ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTGgtaagtcctc ... tttctggcagGATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
EST: gi|37835126|gb|BJ593138.1|BJ593138
EST:     ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTG                         GATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
genomic: ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTGgtaagtcctc ... tttctggcagGATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
EST: gi|37843582|gb|BJ601590.1|BJ601590
EST:     ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTG                         GATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
genomic: ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTGgtaagtcctc ... tttctggcagGATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
EST: gi|162155093|gb|FC330887.1|FC330887
EST:     ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTG                         GATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
genomic: ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTGgtaagtcctc ... tttctggcagGATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
EST: gi|162267366|gb|FC443909.1|FC443909
EST:     ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTG                         GATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
genomic: ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTGgtaagtcctc ... tttctggcagGATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
EST: gi|37829099|gb|BJ587111.1|BJ587111
EST:     ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTG                         GATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT
genomic: ACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTGgtaagtcctc ... tttctggcagGATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTT

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: 33 (upstream exon), 21 (downstream exon)
Score: 3

GAATGTACCCATTGCGTTTATAAGCGTTATCATATTGCCGATTGTTGGAAACGCCGCAGAGCATGCGAGTGCTATAATGTTTGCCCTCAAAGATAAGCTGgtaagtcctc ... tttctggcagGATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcattggcttcgatttttgtcttcgtcttgttcacatttttctttctggcagGATATCTCGCTTGGGGTGGCTATCGGTTCTTCCACTCAGATCTCTATGTTTGTG
                tttttgtcttcgtctt  CT-rich tract
                                      atttttcttt  TA-rich tract