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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttaatatacactcggcagaactaaaaagtttttagttttacgccttttttttttgttaaaaaaatttcccggtttttcattttcttttttttgtgcagGTTTTATATTTTGATGACACCATTACGGCGTATAGAACTGTGTACTATTCGGGCACATTGCTACCAGTTGCGCTTATTTTACTGGGAAAAGTCGTCAAAC

Basic information

species Physcomitrella patens
transcript PP1S61_93V6.2
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|162256534|gb|FC432844.1|FC432844
EST:     GTTTCTTCTACACCGTGTTAGTGCTCAACTTGACCGTCATGGGTTTCCTG                         GTTTTATATTTTGATGACACCATTACGGCGTATAGAACTGTGTACTATTCG
genomic: GTTTCTTCTACACCGTGTTAGTGCTCAACTTGACCGTCATGGGTTTCCTGgtgagtatct ... ttttgtgcagGTTTTATATTTTGATGACACCATTACGGCGTATAGAACTGTGTACTATTCG
EST: gi|67728055|gb|BJ978314.1|BJ978314
EST:     GTTTCTTCTACACCGTGTTAGTGCTCAACTTGACCGTCATGGGTTTCCTG                         GTTTTATATTTTGATGACACCATTACGGCGTATAGAACTGTGTACTATTCG
genomic: GTTTCTTCTACACCGTGTTAGTGCTCAACTTGACCGTCATGGGTTTCCTGgtgagtatct ... ttttgtgcagGTTTTATATTTTGATGACACCATTACGGCGTATAGAACTGTGTACTATTCG

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-Seq library.


Block sizes: 22 (upstream exon), 14 (downstream exon)
Score: 1

AGCGATACCCAAGAGTAATTTCTTGGCAGTGAAGCTTGGTTCTTTTTTCGGTTTCTTCTACACCGTGTTAGTGCTCAACTTGACCGTCATGGGTTTCCTGgtgagtatct ... ttttgtgcagGTTTTATATTTTGATGACACCATTACGGCGTATAGAACTGTGTACTATTCGGGCACATTGCTACCAGTTGCGCTTATTTTACTGGGAAAAGTCGTCAAAC































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttttttgttaaaaaaatttcccggtttttcattttcttttttttgtgcagGTTTTATATTTTGATGACACCATTACGGCGTATAGAACTGTGTACTATTCGGGCACATTGCTACCAGTTGCGCTTATTTTACTGGGAAAAGTCGTCAAAC
                     tttcccggtttttcat  CT-rich tract
                             tttttcattttctttt  TA-rich tract