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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttgcaatttttttcagttaccacgtaagcgctgagctatgtgtgcttatcacaggacaaaaatgtttttgacaatatacgcacagaagttgcaagattgtattgttacagaattacaaatattatacccggttgatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTTAGCAATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTC

Basic information

species Physcomitrella patens
transcript PP1S58_197V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_197V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ28090 (Selaginella moellendorffii), 3'ss of exon 11
gtactgttgcaatttttttcagttaccacgtaagcgctgagctatgtgtgcttatcacaggacaaaaatgtttttgacaatatacgcacagaagttgcaagattgtattgttacagaattacaaatattatacccggttgatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTTAGCAATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTC
                                                                     ||||  | |     | ||   |   || | |   | || | |     ||| ||   | |  |     ||  || | | ||   ||  | || || |  || || || || ||||||||||||||||| ||||||||||| ||||| ||||| || || |||||||| || ||||||||  
---------------------------------------------------------------------gtttgaggcttagcaagctttgctttttcga---tctagtctcgagtaataacccgtgtgct--tttgtgtatctaacagCAGCTCTTGGGAGACGCCGGCCGAGCAGCCATTCAAACGCAAGGCTCGGTTAGCAATCCGTTCGGGCCAACCTTCGTCTATGGCTACCGAAACATCGCAT

upper sequence: PP1S58_197V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ29519 (Selaginella moellendorffii), 3'ss of exon 11
gtactgttgcaatttttttcagttaccacgtaagcgctgagctatgtgtgcttatcacaggacaaaaatgtttttgacaatatacgcacagaagttgcaagattgtattgttacagaattacaaatattatacccggttg-atgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTTAGCAATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTC
                                                                        |||||   | |||   ||    ||||    |     |  |   || | | ||    | | |     || || | | ||   ||  | || || |  || || || || ||||||||||||||||| ||||||||||| ||||| ||||| || || |||||||| || ||||||||  
-----------------------------------------------------------------------gtttgaggct-tac---caagctttgctttttctatctagtctcgagtaataacccgtgtgcttttgtgtatctaacagCAGCTCTTGGGAGACGCCGGCCGAGCAGCCATTCAAACGCAAGGCTCGGTTAGCAATCCGTTCGGGCCAACCTTCGTCTATGGCTACCGAAACATCGCAT
















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|67701566|gb|BJ961799.1|BJ961799
EST:     GAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: GAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|208382909|gb|DC928334.1|DC928334
EST:     ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|67726513|gb|BJ976772.1|BJ976772
EST:     ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|6167306|gb|AW145570.1|AW145570
EST:     TGGAAATCAAAGGCGTATCACTGCCAACACCAATTG-AGTTGAAGTGCAG                         GGCCTACTNG-CGATGGTGGGTCGTGCTGCAATTCAA-CGCAAGGCTCTGT
genomic: TGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGT-GAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGG-TCGTGCTGCAATTCAAACGCAAGGCTCTGT
EST: gi|37823222|gb|BJ581288.1|BJ581288
EST:     ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|37836886|gb|BJ594894.1|BJ594894
EST:     ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|208370963|gb|DC944338.1|DC944338
EST:     ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|162176258|gb|FC352715.1|FC352715
EST:     ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|18337725|gb|BJ169749.1|BJ169749
EST:     GGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: GGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|37842901|gb|BJ600909.1|BJ600909
EST:     ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|162155578|gb|FC331529.1|FC331529
EST:     ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
EST: gi|37821349|gb|BJ579415.1|BJ579415
EST:     ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAG                         GGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT
genomic: ATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTT

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: 13

GTGATGGTGGTGAGGAACTTGACAAAGCTGCTTACGCTGATGGAAATCAAAGGCGTATCACTGCCAACACCAAATGGAGTGAAGTGCAGgtactgttgc ... gatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTTAGCAATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaagattgtattgttacagaattacaaatattatacccggttgatgttatagGGCCTACTAGGCGATGGTGGTCGTGCTGCAATTCAAACGCAAGGCTCTGTTAGCAATCCATTCGGTCCAACGTTTGTGTATGGCTATCGCAACATCGCTC
                                         ggttgat  putative branch site (score: 13)
           tattgttacagaatta  TA-rich tract