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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcctttgtttttctgaactgcttgttcttgtcacattatcttttgcttgcaatttcaatcagatgaaagatgcctcacaccacctccattttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGACTCACAAAGGGTTTGTTTCTGACCAGAAACTTGGATCCTCAGATAGTTGA

Basic information

species Physcomitrella patens
transcript PP1S180_67V6.1
intron # 10
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|162254586|gb|FC429436.1|FC429436
EST:     TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAA                         GTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
genomic: TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
EST: gi|208365735|gb|DC944163.1|DC944163
EST:     TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAA                         GTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
genomic: TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
EST: gi|162220966|gb|FC396151.1|FC396151
EST:     TGTNTAGTGGAGTGCCTTC-AACTTGTTGTTCAGAGAACAACCCTCCCCA                         GTATCCACCCATGACAAGTGGAAAC
genomic: TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAAC
EST: gi|67698972|gb|BJ959205.1|BJ959205
EST:     TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAA                         GTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
genomic: TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
EST: gi|18340553|gb|BJ172581.1|BJ172581
EST:     TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAA                         GTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
genomic: TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
EST: gi|208364966|gb|DC947108.1|DC947108
EST:     TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAA                         GTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
genomic: TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
EST: gi|162220965|gb|FC396150.1|FC396150
EST:     TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAA                         GTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
genomic: TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
EST: gi|37821493|gb|BJ579559.1|BJ579559
EST:     TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAA                         GTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
genomic: TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
EST: gi|18340752|gb|BJ172783.1|BJ172783
EST:     TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAA                         GTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC
genomic: TGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGAC

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), 33 (downstream exon)
Score: 8

ATACCCTTCTTCTTTGAGCCCAATTATGACTGTTTAGTGGAGTGCCTTCCAACTTGTTGTTCAGAGAACAACCCTCCCAAgtgagcctta ... ttttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGACTCACAAAGGGTTTGTTTCTGACCAGAAACTTGGATCCTCAGATAGTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttgcaatttcaatcagatgaaagatgcctcacaccacctccattttctgcagGTATCCACCCATGACAAGTGGAAACCACCTTTTGAGCAAGTACAAACAGACTCACAAAGGGTTTGTTTCTGACCAGAAACTTGGATCCTCAGATAGTTGA
                            gcctcac  putative branch site (score: 8)
                                    ccacctccattttct  CT-rich tract
       aatttcaat  TA-rich tract