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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttccctgtcgttttgtaatcgagaaggttatgtattagtgattcttttatcaacttgagcgtgctctttatttctgtagaaaatttgtcaagtggcgggtgtagaatagtagtcattatgcacctataggagacaaatttccaggtgtcttcaatgaagtaagtttctcttttctccctcatgatggtagGATAAAGCAGAGGCTACATCGAAGGCAATGCCTGCCAGCAACGTTCTTTCGAGGTCGCCAATGCCGATGTATTCCCCTCCCATCGACAACGACGACGGGA

Basic information

species Physcomitrella patens
transcript PP1S396_7V6.1
intron # 3
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|208377971|gb|DC906914.1|DC906914
EST:     GACGAAAAGATGAGGTGCAAACCGCGACTAAGAAGACCAAGGACAAAAAG                         GATAAAGCAGAGGCTACATCGAAGGCAATGCCTGCCAGCAACGTTCTTTCG
genomic: GACGAAAAGATGAGGTGCAAACCGCGACTAAGAAGACCAAGGACAAAAAGgtaattttcc ... atgatggtagGATAAAGCAGAGGCTACATCGAAGGCAATGCCTGCCAGCAACGTTCTTTCG




















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: 34 (upstream exon), 31 (downstream exon)
Score: 14

AAGAAGGAGAATGGGAAGAGACGAAAAGATGAGGTGCAAACCGCGACTAAGAAGACCAAGGACAAAAAGgtaattttcc ... atgatggtagGATAAAGCAGAGGCTACATCGAAGGCAATGCCTGCCAGCAACGTTCTTTCGAGGTCGCCAATGCCGATGTATTCCCCTCCCATCGACAACGACGACGGGA































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttccaggtgtcttcaatgaagtaagtttctcttttctccctcatgatggtagGATAAAGCAGAGGCTACATCGAAGGCAATGCCTGCCAGCAACGTTCTTTCGAGGTCGCCAATGCCGATGTATTCCCCTCCCATCGACAACGACGACGGGA
                            tttctcttttctccct  CT-rich tract
                        taagttt  TA-rich tract