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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCGAGGTTTTGAGTTTGCCAAAGCTGTGACGTTGATTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctgatttattctcatccagaagtgcatttcctgaagaaatgatctgcagttttccttggattttctccttattgttcaactaataaatgaagatcaatgatttagaatgaatttgggtatgtgcag

Basic information

species Physcomitrella patens
transcript PP1S408_23V6.1
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 24
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 22
TTGCGAGGTTTTGAGTTTGCCAAAGCTGTGACGTTGATTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaac--tctgatttattctcatccagaagtgcatttcctgaagaaatgat----ctgcag-ttttccttggattttctccttat-tgttcaactaataaatgaagatcaatgatttagaatgaatttgggtatgtgcag
||| |||||||||| ||||||||||||||||| ||| | | |||||||||  | || || ||||   ||||||| || ||  |||||| ||   |   |||||      |    || |  |      | ||| |  ||      ||||  | |   || ||| ||| |||   |||||  | |                                            
TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgttcttccag-------------------------------------------
















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|162231516|gb|FC407966.1|FC407966
EST:     TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAG                         GTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
genomic: TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctga ... gtatgtgcagGTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
EST: gi|67579410|gb|BJ951531.1|BJ951531
EST:     TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAG                         GTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
genomic: TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctga ... gtatgtgcagGTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
EST: gi|67578962|gb|BJ951113.1|BJ951113
EST:     TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAG                         GTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
genomic: TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctga ... gtatgtgcagGTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
EST: gi|162171191|gb|FC346362.1|FC346362
EST:     TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAG                         GTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
genomic: TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctga ... gtatgtgcagGTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
EST: gi|162269122|gb|FC444990.1|FC444990
EST:     TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAG                         GTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
genomic: TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctga ... gtatgtgcagGTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
EST: gi|19778765|gb|BQ039356.1|BQ039356
EST:     TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAG                         GTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
genomic: TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctga ... gtatgtgcagGTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
EST: gi|37848450|gb|BJ606458.1|BJ606458
EST:     TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAG                         GTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
genomic: TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctga ... gtatgtgcagGTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
EST: gi|162163688|gb|FC340287.1|FC340287
EST:     TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAG                         GTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG
genomic: TTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctga ... gtatgtgcagGTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATG

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: 29 (upstream exon), 35 (downstream exon)
Score: 15

TTGCGAGGTTTTGAGTTTGCCAAAGCTGTGACGTTGATTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaactctga ... gtatgtgcagGTGAAGCGACCCCAAGCTAAGGCTCGCTTTGCAACGGCCATTGCAGAAATGTATTCTGAGATTGCAGCTAAGGAGGAATCTCACCTGCCGTTGCGATCCA




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