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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAGCTTTGTACATGGCAGCGGAGGCAAATAATCCTTACTTTCGTTTGGGCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAGgtagtttacctgccaatttttatccttaaggtgtcgattcttgcatactagtgtggagtgatgagaaaatttcaatgataaacctctttgcatcggattgcactcggaataatttagcgcgccttggactaatttggagatgatgtttgtgtag

Basic information

species Physcomitrella patens
transcript PP1S114_207V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S114_207V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv19s0090g01000.t01 (Vitis vinifera), 5'ss of exon 5
ACTAGCTTTGTACATGGCAGCGGAGGCAAATAATCCTTACTTTCGTTTGGGCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAGgtagtttacctgccaatttttatccttaaggtgtcgattcttgcatactagtgtggagtgatgagaaaatttcaatg--ataaacctctttgcatcggattgcactcggaataatttagcgcgccttggactaatttggagatgatgtttgtgtag
 || ||  |  ||||||| | ||| |||   ||||| || || || ||||| ||||||||| | |||||||||||||| ||||||||| | || ||||||||   || ||  |  |  |||   ||  |    | | | ||   | | | |        | | |  |||| | |||   ||||   || | | | | |                                                          
GCTTGCCCTTGACATGGCTGTGGAAGCAGGAAATCCATATTTCCGGTTGGGTTACAACAGCTTGGGTGCATTTGCTACCATCAACCACCTTCACTTTCAGgtttctttccacctcacctttgaactgcaatcattg-tactataaaattggctccattggttaatgaaatatgaattccataactttcatggtaacag----------------------------------------------------------
















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|162170578|gb|FC347074.1|FC347074
EST:     GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAG                         GCATATTACTTGGCTGCCCCCTTTCCCAT
genomic: GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAGgtagtttacc ... gtttgtgtagGCATATTACTTGGCTGCCCCCTTTCCCAT
EST: gi|162153465|gb|FC329351.1|FC329351
EST:     GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAG                         GCATATTACTTGGCTGCCCCCTTTCCCATTGAAAGAGCACCCGCTACTAGA
genomic: GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAGgtagtttacc ... gtttgtgtagGCATATTACTTGGCTGCCCCCTTTCCCATTGAAAGAGCACCCGCTACTAGA
EST: gi|100376965|gb|BY949552.1|BY949552
EST:     GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAG                         GCATATTACTTGGCTGCCCCCTTTCCCATTGAAAGAGCACCCGCTACTAGA
genomic: GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAGgtagtttacc ... gtttgtgtagGCATATTACTTGGCTGCCCCCTTTCCCATTGAAAGAGCACCCGCTACTAGA
EST: gi|67568739|gb|BJ941563.1|BJ941563
EST:     GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAG                         GCATATTACTTGGCTGCCCCCTTTCCCATTGAAAGAGCACCCGCTACTAGA
genomic: GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAGgtagtttacc ... gtttgtgtagGCATATTACTTGGCTGCCCCCTTTCCCATTGAAAGAGCACCCGCTACTAGA
EST: gi|162159010|gb|FC334844.1|FC334844
EST:     GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAG                         GCATATTACTTGGCTGCCCCCTTTCCCATTGAAAGAGCACCCGCTACTAGA
genomic: GCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAGgtagtttacc ... gtttgtgtagGCATATTACTTGGCTGCCCCCTTTCCCATTGAAAGAGCACCCGCTACTAGA

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), 35 (downstream exon)
Score: 92

ACTAGCTTTGTACATGGCAGCGGAGGCAAATAATCCTTACTTTCGTTTGGGCTACAACAGCCTTGGTGCATTTGCTACAATCAACCACTTGCATTTTCAGgtagtttacc ... gtttgtgtagGCATATTACTTGGCTGCCCCCTTTCCCATTGAAAGAGCACCCGCTACTAGAGTGTCTTACGGCAGGAAGAAGAGTGGTGTGAAAGTGTATGAACTCACGA




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