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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgacttttacctgtggatttgaattttatgtagcttgtcttcggatcatagtagggatagtcttttgattcttttgcaggcttcctttttttaacccagctaatctagtgagcctgggtgacttgcctctggtatttgataactttgtatttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG

Basic information

species Physcomitrella patens
transcript PP1S223_50V6.1
intron # 4
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|162155717|gb|FC331330.1|FC331330
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|162185524|gb|FC361248.1|FC361248
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|37828398|gb|BJ586410.1|BJ586410
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|208361643|gb|DC950331.1|DC950331
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|67692304|gb|BJ952537.1|BJ952537
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|162172649|gb|FC348030.1|FC348030
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|162180018|gb|FC356089.1|FC356089
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|37842788|gb|BJ600796.1|BJ600796
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|162190854|gb|FC368052.1|FC368052
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|208372257|gb|DC948060.1|DC948060
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|18335076|gb|BJ167094.1|BJ167094
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|162200375|gb|FC376660.1|FC376660
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|37836649|gb|BJ594657.1|BJ594657
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|208389164|gb|DC945740.1|DC945740
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|208365828|gb|DC951063.1|DC951063
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|18337537|gb|BJ169561.1|BJ169561
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|37851326|gb|BJ609334.1|BJ609334
EST:     TGTTGACAAGNCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACNTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|162200361|gb|FC376659.1|FC376659
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|162174414|gb|FC350485.1|FC350485
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
EST: gi|208365900|gb|DC951079.1|DC951079
EST:     TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAG                         GTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG
genomic: TGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATG

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: 35 (upstream exon), 16 (downstream exon)
Score: 4

GTGGATATCTACTCATTGTCTCGCTCATGGAAGGAACTTGTTGACAAGGCCCGCGCAAAGCAGCTTTCACCGGCAGAGTACAACTCAGgtctgacttt ... ttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgagcctgggtgacttgcctctggtatttgataactttgtatttggtttcagGTACCTTTGTTCTATCGAACCTTGGAATGTTCGGAGTAGACCGATTTGATGCAATTCTCCCTCCCGGCATG
                               tgataac  putative branch site (score: 4)
                           tatttgataacttt  TA-rich tract