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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatattgttaattgtgcttacgcactttcgagaagggagtttgattcggacgaggttaaatcgaacattgtaactcacttcgtgttggtgtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTTTAAGGCCTTTTATGAGCTCTTCACTACTATTGATAAGCTAACTGTAGAT

Basic information

species Physcomitrella patens
transcript PP1S2_377V6.1
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|208351144|gb|DC921362.1|DC921362
EST:     ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAG                         CGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
genomic: ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
EST: gi|15326922|gb|BI487306.1|BI487306
EST:     ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAG                         CGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
genomic: ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
EST: gi|162187025|gb|FC363431.1|FC363431
EST:     ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAG                         CGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
genomic: ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
EST: gi|208388832|gb|DC945408.1|DC945408
EST:     ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAG                         CGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCNATCGACACTT
genomic: ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
EST: gi|162213750|gb|FC390365.1|FC390365
EST:     ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAG                         CGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
genomic: ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
EST: gi|208381823|gb|DC923389.1|DC923389
EST:     ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAG                         CGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
genomic: ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
EST: gi|162255177|gb|FC431487.1|FC431487
EST:     ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAG                         CGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
genomic: ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
EST: gi|37847013|gb|BJ605021.1|BJ605021
EST:     ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAG                         CGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
genomic: ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
EST: gi|18332745|gb|BJ164758.1|BJ164758
EST:     ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAG                         CGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT
genomic: ATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTT

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: 30 (upstream exon), 20 (downstream exon)
Score: 2

GTAATGATATGGGTTGTGGGTCCACAATTGGCCCAATTCTTGCTTCTGGTATTGGCATTCGGACGGTGGACGTTGGCATGCCTCAATTATCCATGCACAGgtatgctcta ... gtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTTTAAGGCCTTTTATGAGCTCTTCACTACTATTGATAAGCTAACTGTAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcggacgaggttaaatcgaacattgtaactcacttcgtgttggtgtacttgcagCGTACGAGAAATGTGCGGAACTGAGGATGTAGACCTCTCCTATCGACACTTTAAGGCCTTTTATGAGCTCTTCACTACTATTGATAAGCTAACTGTAGAT
                           aactcac  putative branch site (score: 2)
           ttaaat  TA-rich tract