Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAAGGATCATACGCCTACCGTGTGGTATGCGAGTAACGGCGAGCGATTGGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattcttatggactaaccttagacatgttagcgttgtcctcgagaaggaacgagggtttctagagcgtttggtgtcttaacccctcaaaccagggcgacctataggaggaatggtgttcggttgattggtgtgtgtgaatgaactcctgtgtgcactggtcgtcgcgttcag

Basic information

species Physcomitrella patens
transcript PP1S65_136V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ10670 (Selaginella moellendorffii), 5'ss of exon 1
GCGAAGGATCATACGCCTACCGTGTGGTATGCGAGTAACGGCGAGCGATTGGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattcttatggactaaccttagacatgttagcgttgtcctcgagaaggaacgagggtttctagagcgtttggtgtcttaacccctcaaaccagggcgacctataggaggaatggtgttcggttgattggtgtgtgtgaatgaactcctgtgtgcactggtcgtcgcgttcag
|| |||||||| |  || || |||||||| |     || || |||||  | || || ||||  |||||||| || |||||||||||||||||||| || ||||||      |     ||     ||  ||   | |||  |  | |  |  |                                                                                                                            
GCCAAGGATCACAATCCCACTGTGTGGTACGGCCACAATGGTGAGCGGCTCGGGACTTACAGAGGCCACAATGGAGCTGTGTGGTGTTGCGATGTCTCAAgtaagtgatccagaatttag----agggataaaatcgtaattttgggaacag----------------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S65_136V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ07495 (Selaginella moellendorffii), 5'ss of exon 1
GCGAAGGATCATACGCCTACCGTGTGGTATGCGAGTAACGGCGAGCGATTGGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattcttatggactaaccttagacatgttagcgttgtcctcgagaaggaacgagggtttctagagcgtttggtgtcttaacccctcaaaccagggcgacctataggaggaatggtgttcggttgattggtgtgtgtgaatgaactcctgtgtgcactggtcgtcgcgttcag
|| |||||||| |  || || |||||||| |     || || |||||  | || || ||||  |||||||| || |||||||||||||||||||| || ||||||      |     |      ||  ||   | |||  |  | |  |  |                                                                                                                            
GCCAAGGATCACAATCCCACTGTGTGGTACGGCCACAATGGTGAGCGGCTTGGGACTTACAGAGGCCACAATGGAGCTGTGTGGTGTTGCGATGTCTCAAgtaagtgatccagaatttgg----agggataaaatcgtaattttgggaacag----------------------------------------------------------------------------------------------------------------------------
















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|162154179|gb|FC330622.1|FC330622
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|18350031|gb|BJ182082.1|BJ182082
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|162191097|gb|FC367359.1|FC367359
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|100383860|gb|BY987117.1|BY987117
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|67576389|gb|BJ949213.1|BJ949213
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTG
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTG
EST: gi|18326502|gb|BJ158501.1|BJ158501
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|208349819|gb|DC905943.1|DC905943
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|18349758|gb|BJ181808.1|BJ181808
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|162157954|gb|FC334407.1|FC334407
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|100370891|gb|BY968106.1|BY968106
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|100376290|gb|BY986114.1|BY986114
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|162183539|gb|FC359013.1|FC359013
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|67709697|gb|BJ965513.1|BJ965513
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|162262027|gb|FC437874.1|FC437874
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|162206923|gb|FC383500.1|FC383500
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|100410803|gb|BY956195.1|BY956195
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|18357972|gb|BJ190031.1|BJ190031
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|100408727|gb|BY974257.1|BY974257
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|18343909|gb|BJ175947.1|BJ175947
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|162152350|gb|FC328537.1|FC328537
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|18342688|gb|BJ174723.1|BJ174723
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|18359045|gb|BJ191105.1|BJ191105
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|100407998|gb|BY955872.1|BY955872
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
EST: gi|18353481|gb|BJ185536.1|BJ185536
EST:     GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCA                         GGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT
genomic: GGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTAT

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), 33 (downstream exon)
Score: 17

GCGAAGGATCATACGCCTACCGTGTGGTATGCGAGTAACGGCGAGCGATTGGGCACGTACAAGGGCCACAACGGGGCTGTGTGGTGTTGCGATGTTTCCAgtaagattct ... tcgcgttcagGGGATTCGACACGCTTGGTGACGAGCTCGGCTGATCAAACTGTGAAGCTATGGGAGTGCGAGACTGGAGTCCTGCTGCACACGTTCAATTTTGATGCGCC




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