Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTAGGGGTGTCGAAGAGTGCATCGCAAGATGAGCTGAAGAGAGCTTACAGGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggtgtttggatgggcgttgctctgtagtttgtcagtgagccacgtgcggaatgcttaatattttgaagttggcacttcaaggagatcgtgctttgtggagtcggtgttctcgtttgtaaatatcatatatacctgcttacttgagtgatctttttcgcag

Basic information

species Physcomitrella patens
transcript PP1S174_37V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S174_37V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os02g43930.3 (Oryza sativa), 5'ss of exon 2
TCTAGGGGTGTCGAAGAGTGCATCGCAAGATGAGCTGAAGAGAGCTTACAGGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggtgtttggatgggcgttgctctgtagtttgtcagtgagccacgtgcgg--aatgcttaatattttgaagttggcacttcaaggagatcgtgctttgtggagtcggtgttctcgtttgtaaatatcatatatacctgcttacttgagtgatctttttcgcag
 || || || || ||||  ||| | || ||||||||||||| ||| ||| | || || || ||||||||||| || ||||||||||| ||||||||||||||  |  |       | |     ||  |||    ||   | ||  |    ||  ||   | | || |  ||||   | | |  |                                                                                     
GCTTGGTGTATCTAAGACAGCAACCCAGGATGAGCTGAAGAAAGCGTACCGTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggacaaacagttctatatttgtctactcttgaactgttggtttggtttggttgacgttttactttttatggcttggtcag-----------------------------------------------------------------------------------

upper sequence: PP1S174_37V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G118731_T01 (Zea mays), 5'ss of exon 2
TCTAGGGGTGTCGAAGAGTGCATCGCAAGATGAGCTGAAGAGAGCTTACAGGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggtgtttggatgggcgttgctctgtagtttgtcagtgagccacgtgcggaatgcttaatattttgaa-gttggcacttcaaggagatcgtgctttgtggagtcggtgttctcgtttgtaaatatcatatatacctgcttacttgagtgatctttttcgcag
||| || ||||| ||||  |||   || |||||||| |||| ||| ||||| || || || || ||||||||||| ||||||||||| ||||||||||||||  |||  |||    ||     ||| |||||| |   | ||      | ||||  |||  |   | || | |  |   |   |||   ||    |  ||| |  |                                                              
TCTTGGTGTGTCTAAGACCGCAAGTCAGGATGAGCTTAAGAAAGCATACAGAAAAGCTGCCATAAAAAACCATCCTGATAAGGGTGGAGACCCTGAGAAGgtttgttc-tgtccacat-----ttgttctgtaat--attagcttagtatgtgc--aattgtaggtgttctcatcgccaggttttccttgatgatgaacttggcag--------------------------------------------------------------
















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|100384816|gb|BY969551.1|BY969551
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|100402414|gb|BY954824.1|BY954824
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|162153711|gb|FC329114.1|FC329114
EST:     GGAAGGCGGCAATTAAGAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|18325240|gb|BJ157236.1|BJ157236
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|162152004|gb|FC327918.1|FC327918
EST:     GGAAGGCGGCAATTAAGAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|162197042|gb|FC375241.1|FC375241
EST:     GGAAGGCGGCAATTAAGAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|162180092|gb|FC356657.1|FC356657
EST:     GGAAGGCGGCAATTAAGAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|208373708|gb|DC936535.1|DC936535
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|67574368|gb|BJ947192.1|BJ947192
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|18346826|gb|BJ178871.1|BJ178871
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGAC
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGAC
EST: gi|208358355|gb|DC934548.1|DC934548
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|162213966|gb|FC390165.1|FC390165
EST:     GGAAGGCGGCAATTAAGAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|18348556|gb|BJ180605.1|BJ180605
EST:     GGAAGGCGGCGATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGGCCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|162151466|gb|FC326971.1|FC326971
EST:     GGAAGGCGGCAATTAAGAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|100384387|gb|BY969518.1|BY969518
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|100407617|gb|BY991778.1|BY991778
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|208353142|gb|DC910151.1|DC910151
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|18343570|gb|BJ175608.1|BJ175608
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|208359865|gb|DC934866.1|DC934866
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|100441954|gb|BY981177.1|BY981177
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|18365920|gb|BJ197998.1|BJ197998
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACC
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACC
EST: gi|162263312|gb|FC439094.1|FC439094
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|18332502|gb|BJ164515.1|BJ164515
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|162166513|gb|FC343210.1|FC343210
EST:     GGAAGGCGGCAATTAAGAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|100392962|gb|BY989694.1|BY989694
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|67569005|gb|BJ941829.1|BJ941829
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|18343937|gb|BJ175976.1|BJ175976
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
EST: gi|100396849|gb|BY953858.1|BY953858
EST:     GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAG                         TTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA
genomic: GGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGA

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), 31 (downstream exon)
Score: 50

TCTAGGGGTGTCGAAGAGTGCATCGCAAGATGAGCTGAAGAGAGCTTACAGGAAGGCGGCAATTAAAAACCATCCGGATAAGGGTGGTGACCCTGAGAAGgtacgttggt ... tttttcgcagTTCAAAGAGATTTCACAAGCGTACGAAGTTTTAAGCGACCCCGAGAAGCGAGAACTGTATGATCAGTATGGAGAAGACGCTCTCAAGGAAGGAATGGGTG




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