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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttctaaacttttaaactatcttccggtttcgagtttgatattgcacacaagacctctgtcttattgcgaaatatagtagggtgaaacatattgattggtatatacttttggatgttttatcagGTTCCCAGTTGATGATAATGGTACCTTGAAGTCTGTTACCGACTATTTTCGGGAGACGTATGGCTATGTTATCCGGCATCCATCTTTGCCTTGCCTCCAA

Basic information

species Physcomitrella patens
transcript PP1S7_194V6.1
intron # 6
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|150170643|gb|ES492180.1|ES492180
EST:     CGCAAGTACCGCATATCTGGGCTTACAAATCAGGCCACCAATGAATTGGA                         GTTCCCAGTTGATGATAATGGTACCTTGAAGTCTGTTACCGACTATTTTCG
genomic: CGCAAGTACCGCATATCTGGGCTTACAAATCAGGCCACCAATGAATTGGAgtgcgttcta ... gttttatcagGTTCCCAGTTGATGATAATGGTACCTTGAAGTCTGTTACCGACTATTTTCG
EST: gi|162272458|gb|FC449071.1|FC449071
EST:     GGGCTTACAAATCAGGCCACCAATGAATTGGA                         GTTCCCAGTTGATGATAATGGTACCTTGAAGTCTGTTACCGACTATTTTCG
genomic: GGGCTTACAAATCAGGCCACCAATGAATTGGAgtgcgttcta ... gttttatcagGTTCCCAGTTGATGATAATGGTACCTTGAAGTCTGTTACCGACTATTTTCG

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), 21 (downstream exon)
Score: 2

AAGCTCTTCGTGGAGTTAAAGTGGAAGTGACTCATCGCGGAAGTATGCGTCGCAAGTACCGCATATCTGGGCTTACAAATCAGGCCACCAATGAATTGGAgtgcgttcta ... gttttatcagGTTCCCAGTTGATGATAATGGTACCTTGAAGTCTGTTACCGACTATTTTCGGGAGACGTATGGCTATGTTATCCGGCATCCATCTTTGCCTTGCCTCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatatagtagggtgaaacatattgattggtatatacttttggatgttttatcagGTTCCCAGTTGATGATAATGGTACCTTGAAGTCTGTTACCGACTATTTTCGGGAGACGTATGGCTATGTTATCCGGCATCCATCTTTGCCTTGCCTCCAA
                    tattgat  putative branch site (score: 2)
                                              ttttatc  putative PPT
                              tatatactttt  TA-rich tract