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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGCGAGACCCTTTGATTGAGTACAAATTAGAGGGTTACAACTTATTTCTGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactcgtgctgcgcatacgccctacttgaagtctctagtgaatctttttcattagtgacccagttcctgctgcctgcgacattaggaggtgaaagttgaccaaaatagtcaccagcatgaaacaaaaattcatagtttaatcgctcaaagttctttcttgcag

Basic information

species Physcomitrella patens
transcript PP1S9_141V6.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_141V6.1 (Physcomitrella patens), 5'ss of exon 19
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 5'ss of exon 18
TCAGCGAGACCCTTTGATTGAGTACAAATTAGAGGGTTACAACTTATTTCTGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactcgtgctgcgcatacgccctacttgaagtctctagtgaatctttttcattagtgacccagttcctgctgcctgcgacattaggaggtgaaagttgaccaaaatagtcaccagcatgaaacaaaaattcatagtttaatcgctcaaagttctttcttgcag
 || ||||| ||| | ||||| || ||| | ||||| || ||  | ||  |||| ||||||||||||||||| || ||||| || ||||||||||| |||||||||    || ||  |  |    | | |  |     |  ||||      ||||  ||| ||   |         || ||| ||||||    |    ||  ||      | || ||                                                   
CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagt--ctgtcctctgactcaaacttgcccggtcctttcagtg------tttctctagagaataaa--------gcatgc-acattacagagaatcagaagagtgctgtggttac---------------------------------------------------

upper sequence: PP1S9_141V6.1 (Physcomitrella patens), 5'ss of exon 19
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 19
TCAGCGAGACCCTTTGATTGAGTACAAATTAGAGGGTTACAACTTATTTCTGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactcgtgctgcgcatacgccctacttgaagtctctagtgaatctttttcattagtgacccagttcctgctgcct-gcgacattaggaggtgaaagttgaccaaaatagtcaccagcatgaaacaaaaattcatagtttaatcgctcaaagttctttcttgcag
 || || || ||  | || ||||| ||  | || || |||||  ||||||||||||||||||||||||| ||  ||||||| ||||||||  | || ||||||  |  |         || |  | || ||| |  || |     ||| ||  |||||   |      ||| |  |   | | | ||                                                                                  
GCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttcttcattaaat----caaaacctctgcttcacttcacacaataat-ttactcattcaagttttgattcttttttttttgtggcag---------------------------------------------------------------------------------
















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|162196312|gb|FC373536.1|FC373536
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162163003|gb|FC338393.1|FC338393
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162172364|gb|FC348305.1|FC348305
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|19789134|gb|BQ041118.1|BQ041118
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162159762|gb|FC336343.1|FC336343
EST:     TGGAAATGATGGCTCANATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTA
EST: gi|162159761|gb|FC336342.1|FC336342
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162184621|gb|FC360819.1|FC360819
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|37828017|gb|BJ586029.1|BJ586029
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162151013|gb|FC327909.1|FC327909
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162175535|gb|FC350966.1|FC350966
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162180612|gb|FC356969.1|FC356969
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162261061|gb|FC436935.1|FC436935
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162262116|gb|FC436871.1|FC436871
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
EST: gi|162175534|gb|FC350965.1|FC350965
EST:     TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAG                         TTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA
genomic: TGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAA

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: 9

TCAGCGAGACCCTTTGATTGAGTACAAATTAGAGGGTTACAACTTATTTCTGGAAATGATGGCTCAAATTCGGCGAAATGTTATATACTCTGTTTACCAGgttagtactc ... tttcttgcagTTTCAACCAGTGATGGCGACGCCTACAGCCGCAAATGGTAGTAGCAAGAAAGACTCGTCTCAAACCAAGGGAAAAGTATCTGCAACTGCAAGTTAAGGCG




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