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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttctcaacctacccgtagaagtccacaatgacttgtggtcatctcagttactctttaacgaagtaattcatcacgatgcgtgttgagctagtaaaagattactctacggatgagggctaaagcatggttcaagattatctgttatgctaaagctttaaactcttctgagatgtaataaacttgtgttatag

Basic information

species Physcomitrella patens
transcript PP1S149_289V6.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 5'ss of exon 15
TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtat-catttctcaacctacccgtagaagt-ccacaatgacttgtggtcatctcagttactctttaacgaagtaattcatcacgatgcgtgttgagctagtaaaagattactctacggatgagggctaaagcatggttcaagattatctgttatgctaaagctttaaactcttctgagatgtaataaacttgtgttatag
||| || || ||| ||||||| ||   ||| ||||| ||| | || ||||||||||||||||| ||||| || || || ||||| ||||||||||||| ||| | ||  || ||   |      |   || || |  |  ||||    ||||| | |  ||   ||| |  | |                                                                                                                              
TGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTTGAAGgtttacaaatcccattttgttttcaattgttcctctcttgcttgct-ccatct-aatggctggataatgctgcag-----------------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GRMZM2G111477_T01 (Zea mays), 5'ss of exon 3
TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttctcaacctacccgtagaagtccacaatgacttgtggtcatctcagttactctttaacgaagtaattcatcacgatgcgtgttgagctagtaaaagattactctacggatgagggctaaagcatggttcaagattatctgttatgctaaagctttaaactcttctgagatgtaataaacttgtgttatag
|||||| |||||| | ||||| ||    ||||| || ||| | || || |||||||| || |||||||| || ||||||||||| || |||||||||| |||    |  |  ||   |   | |    |   ||  |||| ||   ||| |  | ||  ||   | | | || ||  | | |  |                                                                                                                 
TGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTTGAAGgtccggtggc--aagaaagttggatgtcttttcag-gactcgta--catgtttgctaacctaacatgcaatattttgt-atgcag-----------------------------------------------------------------------------------------------------------------

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA10G33680.1 (Glycine max), 5'ss of exon 15
TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgt-atcatttctcaacctacccgtagaagtccacaatgacttgtggtcatctcagttactctttaacgaagtaattcatcacgatgcgtgttgagctagtaaaagattactctacggatgagggctaaagcatggttcaagattatctgttatgctaaagctttaaactcttctgagatgtaataaacttgtgttatag
|||||| |||||| | ||||| ||  | ||| |||| ||  |||||||||| |||||||| || ||||| || || || ||||||||||||||||||| ||| |   ||| ||         |  ||  | ||   |   || |   |||  || |   |||   | |     | ||  || |||   | |    ||  |     |||                                                                                           
TGGTGTTGCTCTTCTCTATGCATCAAGTGAGTTGGATAAGCTTCAAACTGCTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgtttttct-----tttgctgattttcattttagattat--ccatagcattgtttctggtaggtcactactccaca-gatttttctctctctcatcccttatt-------------------------------------------------------------------------------------------

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 15
TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttctcaacctacccgtagaagtccacaatgacttgtggtcatctcagttactctttaacgaagtaattcatcacgatgcgtgttgagctagtaaaagattactctacggatgagggctaaagcatggttcaagattatctgttatgctaaagctttaaactcttctgagatgtaataaacttgtgttatag
|||||| |||||| | ||||| ||   |||| |||| ||| |||||||||| |||||||| |||||||| || || || || |||||||||||||| | |||    ||||||    |       ||  ||| |  |  ||      | ||| | |  |  ||| |  |  | |   |||  | ||   |   | | || |  |||||                                                                                           
TGGTGTTGCTCTTCTATATGCGTCAAAAGAGTTGGATAAACTTCAAACTGCTAACTTTGATCAGAAGATTGGTGTCCAGATTATCCAAAATGCTTTAAAGgttagttttctctgaattttttctgatttcctctttagct------cctctaaatcgcattttgattacattacggatcttg-tggaaggaaaaccagcaccagatt-------------------------------------------------------------------------------------------

upper sequence: PP1S149_289V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 15
TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGg----tatcatttctcaacctacccgtag---aagtccacaatgacttgtggtcatctcagttactctttaacgaagtaattc-atcacgatgcgtgttgagctagtaaaagattactctacggatgagggctaaagcatggttcaagattatctgttatgctaaagcttta--aactcttctgagatgtaataaacttgtgttatag
|||||| |||||| | ||||| ||  | ||| |||| ||  |||||||||| |||||||| || ||||| || || || ||||||||||||||||||| ||    | |  ||  |   |  |     |    |  ||  | ||  | |    ||   |  |  |||  |  ||  |    |||  || |    | | || |  |        |||   | |    |   |  | |  | ||  || |   | | || | |    || | |||  | || |||||| |   |||  |            
TGGTGTTGCTCTTCTTTATGCATCGAGTGAGTTGGATAAGCTTCAAACTGCCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAGgttagtgtttttcttttgctgattttcattttagatcttccatagcattgtttctggtagggcactactccacagatagtttctgtctcctcccttattcacttcaggcctcattctgcaatattttgagcttta--cttgcctctaagatgtatggtttaaccaacccttactacctgttctgacaaaaaatgcag-----------

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|162159174|gb|FC334345.1|FC334345
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162198558|gb|FC373404.1|FC373404
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|208356851|gb|DC926862.1|DC926862
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162192962|gb|FC371945.1|FC371945
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162175003|gb|FC350902.1|FC350902
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162156171|gb|FC332546.1|FC332546
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162192963|gb|FC371946.1|FC371946
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162175002|gb|FC350901.1|FC350901
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|37850096|gb|BJ608104.1|BJ608104
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162268426|gb|FC444195.1|FC444195
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|208369434|gb|DC955895.1|DC955895
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162276484|gb|FC452682.1|FC452682
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162156170|gb|FC332545.1|FC332545
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162183371|gb|FC359286.1|FC359286
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|162268425|gb|FC444194.1|FC444194
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
EST: gi|208366302|gb|DC947546.1|DC947546
EST:     CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGG                         ATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT
genomic: CGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTT

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), 11 (downstream exon)
Score: 4

TGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTTGAGGgtatcatttc ... tgtgttatagATGCCTGCGTACACAATTGCACGCAATGCTGGAGTGGAGGGAGCTGTCGTTGTTGGAAAGCTTATGGAGCAAACAAACATGAGCATTGGATATGATGCTG




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