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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctggtaggatgctggttatctgatttatcgcttagattaatttcaattcaactttcggtcggtgattggctgaattgattactttgaacgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG

Basic information

species Physcomitrella patens
transcript PP1S83_162V6.1
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|18329713|gb|BJ161719.1|BJ161719
EST:     GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAG                         GTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
genomic: GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
EST: gi|208347445|gb|DC909752.1|DC909752
EST:     GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAG                         GTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
genomic: GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
EST: gi|18372591|gb|BJ204193.1|BJ204193
EST:     GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAG                         GTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
genomic: GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
EST: gi|18356123|gb|BJ188182.1|BJ188182
EST:     GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAG                         GTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
genomic: GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
EST: gi|18354019|gb|BJ186074.1|BJ186074
EST:     GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAG                         GTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
genomic: GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
EST: gi|18349502|gb|BJ181551.1|BJ181551
EST:     GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAG                         GTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
genomic: GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
EST: gi|162150536|gb|FC326392.1|FC326392
EST:     GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAG                         GTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
genomic: GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
EST: gi|18349065|gb|BJ181114.1|BJ181114
EST:     GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAG                         GTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
genomic: GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
EST: gi|18345693|gb|BJ177736.1|BJ177736
EST:     GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAG                         GTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
genomic: GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG

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: 26 (upstream exon), 23 (downstream exon)
Score: 4

GGAATGACACGGTTGCTCCTCACTCGCATCCCGCATTTCCGAGAGgtttgttgtt ... cgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattcaactttcggtcggtgattggctgaattgattactttgaacgatgcgcagGTAGTCTTGATGGCCTTTGAATGTCCGCACTGCAACGAAAG
                             aattgat  putative branch site (score: 4)
                             aattgatta  TA-rich tract