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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGGATGAGAAACTATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAGgtatggttatcatcttgcgtttgtgggggtttggatgtgtagtctgcgcgcttgttcgctcccctaagtaattttgaggtttttagactatgtatttatccagtaataagataaggataaaaaacgtactgccgattcaaaattttggtggaattcag

Basic information

species Physcomitrella patens
transcript PP1S70_254V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S70_254V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: AT2G18510.1 (Arabidopsis thaliana), 5'ss of exon 6
GATGTGGATGAGAAACTATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAGgta-tggttatcatcttgcgtttgtgggggtttggatgtgtagtctgcgcgcttgttcgctcccctaagtaattttgaggtttttagactatgtatttatccagtaataagataaggataaaaaacgtactgccgattcaaaattttggtggaattcag
|||||||||||||| || ||||| |||||||||||||| ||||| ||||| |   | || ||||||||| |  || | || |        ||  | |   |||   |  |||       |||   ||||  | |   |||     ||    | | || | ||| |||  ||| |    |  ||| || ||| ||  |    | |    ||||  |          
GATGTGGATGAGAAGCTCTTGTATGATACTTTCAGTGCATTTGGTGTGATTGCTTCTAATCCTAAGgtagtattttttatttcattagattgtagttcatgattcttgatctctttatctgt---ctcctgtcaccgattcgatagt----aaattagg-attcatc-ggtattccactgtggagaataaatgt--tagaaacttttcatttcag----------

upper sequence: PP1S70_254V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 5'ss of exon 6
GATGTGGATGAGAAACTATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAGgtatggttatcatcttgcgtttgtgggggtttggatgtgtagtctgcgcgcttgttcgctcccctaagtaattttgaggtttttagactatgtatttatccagtaataagataaggataaaaaacgtactgccgattcaaaattttggtggaattcag
|||||||||||||||||  |||| |||||||||||||| ||||| || || |||||||| || |||||   |    |   ||   |||       ||||    | ||   | | |   | ||  ||    || | ||     ||  ||  |  || |     |  |||    |||                                                 
GATGTGGATGAGAAACTTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAGgt---gacgcctcttttgattttcccttttttgagaatata---tacacatatattttctgttatatggaacc---agaattggaatctctccccatccccaccc-taac------------------------------------------------
















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|100368483|gb|BY967035.1|BY967035
EST:     TATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAG                         ATCATGAGGGATCCAGATTCTGGGTA-TTCGCGAGGATTTGGCTTCATCAG
genomic: TATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAGgtatggttat ... tggaattcagATCATGAGGGATCCAGATTCTGG-TAATTCGCGAGGATTTGGCTTCATCAG
EST: gi|162152540|gb|FC328818.1|FC328818
EST:     TATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAG                         ATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCAGC
genomic: TATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAGgtatggttat ... tggaattcagATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCAGC
EST: gi|208375791|gb|DC936731.1|DC936731
EST:     TATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAG                         ATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCAGC
genomic: TATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAGgtatggttat ... tggaattcagATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCAGC
EST: gi|208357964|gb|DC938835.1|DC938835
EST:     TATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAG                         ATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCANC
genomic: TATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAGgtatggttat ... tggaattcagATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCAGC
EST: gi|162171578|gb|FC347519.1|FC347519
EST:     GATAGTCACAAACCCTAAG                         ATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCAGC
genomic: GATAGTCACAAACCCTAAGgtatggttat ... tggaattcagATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCAGC

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), 34 (downstream exon)
Score: 3

GATGTGGATGAGAAACTATTGTACGATACTTTCAGTGCCTTTGGCGTGATAGTCACAAACCCTAAGgtatggttat ... tggaattcagATCATGAGGGATCCAGATTCTGGTAATTCGCGAGGATTTGGCTTCATCAGCTACGATTCGTTTGAAGCTTCAGACTCTGCAATTGAG




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