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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgacggactggtcatgccttaagtgattttgttttatgagtgagcttgttctaatatatatatatatatatatatatatatatatatatattttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTCACTCTCTATGGCCAGCTTTATGTGCGCGTCCCCATCGCAGAAGACAAGT

Basic information

species Physcomitrella patens
transcript PP1S131_109V6.1
intron # 11
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|162256295|gb|FC432201.1|FC432201
EST:     GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAA                         GTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
genomic: GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
EST: gi|15730138|gb|BI741692.1|BI741692
EST:     GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAA                         GTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCATTGGTC
genomic: GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
EST: gi|37829835|gb|BJ587847.1|BJ587847
EST:     GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAA                         GTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
genomic: GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
EST: gi|162198158|gb|FC372575.1|FC372575
EST:     GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAA                         GTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
genomic: GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
EST: gi|162158731|gb|FC335579.1|FC335579
EST:     GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAA                         GTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
genomic: GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
EST: gi|162151296|gb|FC327737.1|FC327737
EST:     GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAA                         GTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
genomic: GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
EST: gi|162151297|gb|FC327738.1|FC327738
EST:     GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAA                         GTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
genomic: GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
EST: gi|162198157|gb|FC372574.1|FC372574
EST:     GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAA                         GTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
genomic: GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
EST: gi|37835292|gb|BJ593304.1|BJ593304
EST:     GAATGCCTGAGAATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAA                         GTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC
genomic: GAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTC

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: 22 (upstream exon), 35 (downstream exon)
Score: 13

GTCCGGATCCAATGTGAGCCTGGAGGCAGGCTAGTGATTGCTGGAATGCCTGAGGATCCAGAGAATCCCTGGGGCGTGACACCTTTCAGAAAAgtaagtttcc ... attttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTCACTCTCTATGGCCAGCTTTATGTGCGCGTCCCCATCGCAGAAGACAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttctaatatatatatatatatatatatatatatatatatatattttctcagGTCATAAGTTTACCCTCTCGAATCGATGCACATCAAACATCAGCAGTGGTCACTCTCTATGGCCAGCTTTATGTGCGCGTCCCCATCGCAGAAGACAAGT
    ttctaat  putative branch site (score: 13)
                                            tattttctc  putative PPT
       taatatatatatatat  TA-rich tract