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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgctaattcgattgggattcttcaatctcatcgagattttgaattggtctcattaaacgatcaaaaaccttctttcacacaactctggggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTGATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCA

Basic information

species Physcomitrella patens
transcript PP1S180_67V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S180_67V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 5
gattgctaattcgattgggattcttcaatctcatcgagattttgaattggtctcattaaacgatcaaaaaccttctttcacacaactctggggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTGATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCA
      | | | ||||     || |||| ||  |    ||||  || ||     |    |       |    || |  |      |  |  |||   || ||     |||     |||||   |||||||||||| | ||||| |||||||| |||||||||||||| ||  | || || || || || |  || || ||
-----gtcactggattcta--tcatcaaacttgt-accatttaaaactgtatataactcatatcgtgatgggttttcccctttttccatcagGT---CAAATCTCTGATC---CCTTGAAG--GGAATATATGGAGCAGGTGCACATTCTGACTATGGCCTGATTACCCTCTTGGCAACAGATGATGTCCTAGGACTTCA
















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|162254586|gb|FC429436.1|FC429436
EST:     AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCG                         ATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
genomic: AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
EST: gi|208393130|gb|DC929625.1|DC929625
EST:     AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCG                         ATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
genomic: AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
EST: gi|208365735|gb|DC944163.1|DC944163
EST:     AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCG                         ATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
genomic: AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
EST: gi|162220966|gb|FC396151.1|FC396151
EST:     AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCG                         ATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
genomic: AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
EST: gi|67698972|gb|BJ959205.1|BJ959205
EST:     AGGCATCANTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCG                         ATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTNTG
genomic: AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
EST: gi|208364966|gb|DC947108.1|DC947108
EST:     AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCG                         ATGAGAAATCAAGTGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
genomic: AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
EST: gi|162220965|gb|FC396150.1|FC396150
EST:     AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCG                         ATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
genomic: AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
EST: gi|100417046|gb|BY993217.1|BY993217
EST:     AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCG                         ATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
genomic: AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
EST: gi|37821493|gb|BJ579559.1|BJ579559
EST:     AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCG                         ATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG
genomic: AGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTG

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: 33 (upstream exon), 35 (downstream exon)
Score: 10

CGGTTGATTGCTTTGGCACTCAACCTTGAAGAGACTTACTTCGAGAAGCCAGGCATCACTGATGATCCTATGGCAAGTTTGCGACTTCTTCATTATTCCGgtcagtttga ... gggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTGATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggtctcattaaacgatcaaaaaccttctttcacacaactctggggtgtgcagATGAGAAATCAAATGTTGAACTTGGAATATATGGAACTGGTGCTCATTCTGATTATGGCCTGATTACTCTTCTTGCTACGGACGACGTGCCTGGTCTCCA
       tcattaaa  TA-rich tract