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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgagtagcgtcatattctgtgttgttggtacgggtgtgatgttgagctgtgtgggtctgcgttgagtcgtggcgttctgcgaggtgccaacgaggcatt...

Basic information

species Physcomitrella patens
transcript PP1S306_62V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 5'ss of exon 11
GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgag--tagcgtcatattctgtgttgttggtacgggtgtgatgttgagctgtgtgggtctgcgttgagtcgtggcgttctgcgaggtgccaacgaggcatt---
 ||||    || ||||||||||||||||| |||||  | ||||||||| | || |||||||| |||||| |||| ||||  ||||| ||  ||   |   ||| || |   ||   ||   |    | |||| |    | ||| |  | ||  || |   |  |       |   |      |||    
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaatattggatt-tgagccattttaactaat----tattgaaccagatcggtattaggtggatcatcatgagcacaataatctaatttcctcataaga

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgagtagcgtcatattctgtgttgttggtacgggtgtgatgttgagct-gtgtgggtctgcgttgagtcgtggcgttctgcgaggtg-ccaacgaggcatt
 ||||    || ||||||||||||||||| |||||  | ||||||||||| ||||||||||| ||||| ||||| ||||  ||||| || |      |    | |||   || |      ||||     |  | || | |   ||     | |  |      ||   | ||  ||    ||  |  
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaatttgagat-tgtaactgatgaactagtgaatccaaattagtatagacatgtcgctattgatactaagctcttatgtttcccttcagttaa-

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgag-tagcgtcatattctgtgttgttggtacgggtgtgatgttgagctgtgtgggtctgcgttgagtcgtggcgttctgcgaggtgccaacgaggcatt-------
 |||||||||| || ||||||||||||||||| ||| | || ||||| |||||||||||||| ||||| || || ||||  || || ||      || |  |                  |    |  |  ||||  | ||  |    | | ||      |||| | |    |        ||||       
ATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCAgtaagactaaatcctgctggacaccacaaaactatataatctccttggctgatttggaattttctaactcaaa---ttctacaaaacactttttttccatttgttaag

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 11
GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgagtagcgtcatattctgtgtt------gttggtacgggtgtgatgttgagctgtgtgggtctgcgttgagtcgtggcgttctgcgaggtgccaacgaggcatt
 | ||||| ||||||||||| || ||||| ||||| ||||| ||||| || || ||||||||||| ||||| |||||||  ||||||||||   | || || ||  ||       |   | |  ||||| | |     | ||| | | |    ||  |       |||| | || |   ||| |      
ATATTCCATAAACGCATGCCTCCAGAAGCTGTTGATTTGGTTTCAAGACTACTGCAGTACTCTCCTAATCTACGGTGCACAGCTgtgagtacattaattttttggtttctcataatccattcttgtgtgttctgtctttttgttgctgtttcctgcatttaaaatttcttcaagat--taacaatc----

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 11
GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgagtagcgtcatattctgtgt-tgttggtacgggtgtgatgttgagctgtgtgggtctgcgttgagtcgtggcgttctgcgaggtgccaacgaggcatt
||||||||||| || ||||| ||||||||||| ||||||||||| ||||| |||||||| || || |  || || ||||| || || ||| |   | |  ||  ||   | |||| |   | | |  || |  | |                                                 
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtcgcgttctcgttgagcgctggttca--tttaactttaaatttttcacag-------------------------------------------

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ07216 (Selaginella moellendorffii), 5'ss of exon 11
GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgagtagcgtcatattctgtgttgttggtacgggtgtgatgttgagctgtgtgggtctgcgttgagtcgtggcgttctgcgaggtgccaacgaggcatt
||||||||||| || ||||| ||||||||||| ||||||||||| ||||| |||||||| || || |  || || ||||| || || |||   |||   ||||  ||||   |  | |||      || | || |     | | |   |                                   
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagt--tgtcgcgttct-cgttg--agcgctggttca---tttatcttta-aatttttcacag-----------------------------------

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|162152628|gb|FC328295.1|FC328295
EST:     ACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT                         CTGGAAGCGTGTGTGCACCCGTTCTTTGATGAGCTAAGGGATCCTAACTGC
genomic: ACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgagtagcg ... ctgtttgcagCTGGAAGCGTGTGTGCACCCGTTCTTTGATGAGCTAAGGGATCCTAACTGC




















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: 34 (upstream exon), 35 (downstream exon)
Score: 40

GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgagtagcg ... ctgtttgcagCTGGAAGCGTGTGTGCACCCGTTCTTTGATGAGCTAAGGGATCCTAACTGCCGGCTTCCGAATGGGCGGCCACTGCCCTCTCTGTTCAACTTCAAAACCC




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