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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcacctcttttgggtttaagtttttgtgcagcgtgatgtcgtctgcgcattcgtcgaattcgataaaccttcacggaatgcctaagctgtgactggcttggtttgcagCGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAG

Basic information

species Physcomitrella patens
transcript PP1S218_59V6.1
intron # 7
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|162198108|gb|FC372135.1|FC372135
EST:     ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGG                         CGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
genomic: ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGGgtaagatcac ... tggtttgcagCGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
EST: gi|100448067|gb|CJ972366.1|CJ972366
EST:     ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGG                         CGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
genomic: ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGGgtaagatcac ... tggtttgcagCGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
EST: gi|100374074|gb|BY967923.1|BY967923
EST:     ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGG                         CGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
genomic: ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGGgtaagatcac ... tggtttgcagCGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
EST: gi|162268987|gb|FC445479.1|FC445479
EST:     ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGG                         CGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
genomic: ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGGgtaagatcac ... tggtttgcagCGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
EST: gi|162258201|gb|FC434232.1|FC434232
EST:     ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGG                         CGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
genomic: ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGGgtaagatcac ... tggtttgcagCGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
EST: gi|162264918|gb|FC440693.1|FC440693
EST:     ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGG                         CGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG
genomic: ATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGGgtaagatcac ... tggtttgcagCGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTG

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), 35 (downstream exon)
Score: 61

AGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCATTGGGgtaagatcac ... tggtttgcagCGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaattcgataaaccttcacggaatgcctaagctgtgactggcttggtttgcagCGTATCTTGAGCGTGCAGTACTCCATCCCCGACTATGTGCACATTTCAGTGGAATGCAGGCACTTACTTTCCAGGATATTTGTTGCTAACCCTGCTAAG
         ataaa  TA-rich tract