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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgttcttcaaatgacgtgtaatcattcgtgtggagtctccatgacctctctttgttaactcgttttctaacttacagagagtccatattgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGGATGCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATAC

Basic information

species Physcomitrella patens
transcript PP1S68_29V6.1
intron # 2
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|100390452|gb|BY952860.1|BY952860
EST:     ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAA                         GGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
genomic: ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
EST: gi|208362530|gb|DC931007.1|DC931007
EST:     ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAA                         GGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
genomic: ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
EST: gi|208374670|gb|DC931995.1|DC931995
EST:     ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAA                         GGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
genomic: ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
EST: gi|162264779|gb|FC440346.1|FC440346
EST:     ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAA                         GGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
genomic: ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
EST: gi|18363082|gb|BJ195154.1|BJ195154
EST:     ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAA                         GGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
genomic: ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
EST: gi|162209020|gb|FC385572.1|FC385572
EST:     ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAA                         GGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
genomic: ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
EST: gi|208387224|gb|DC945523.1|DC945523
EST:     ACCCCTGTTT-AATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAA                         GGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
genomic: ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
EST: gi|18329923|gb|BJ161929.1|BJ161929
EST:     ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAA                         GGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
genomic: ACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
EST: gi|208358537|gb|DC946498.1|DC946498
EST:     GTCTCCATCATCCATACAAGAGCTTCTTCTCGCAA                         GGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG
genomic: GTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGG

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: 31 (upstream exon), 23 (downstream exon)
Score: 5

GTGAAGCTGACTGAGTTGCCTAGTCTTCCACCCCTGTTTAAATCGTCTCCATCATCCATACAAGAGCTTCTTCTCGCAAgtatgtgtag ... ttgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGGATGCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctctctttgttaactcgttttctaacttacagagagtccatattgtttgtagGGGATATTTTGGAACATGCTGTAGTTTTGAGTGTGAAAATGGAGGATCAGGATGCATTTGAGCGCCATTTTCTTCAACTCAAGTCATACTACACCGATAC
                                          atattgttt  TA-rich tract