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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctcttcctaattgattttagtgcattgtcacgtcaggctggttctttacaagatttattcaatcctgtagatatggtgattggcgtaaatttcacgtcgctctaactattcgactctgactgatgcag

Basic information

species Physcomitrella patens
transcript PP1S77_89V6.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 5'ss of exon 17
lower sequence: GLYMA03G07460.1 (Glycine max), 5'ss of exon 17
GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctct-tcctaattgattttagtgcattgtcacgtcaggctggttctttacaagatttattcaatcctgtagatatggtgattggcgtaaatttcacgtcgctctaactattcgactctgactgatgcag
||||||||| ||||||| |||||  | ||||| ||||| || ||||| ||||||||||| ||||||   |||      ||||||  |  | | |||| |||   | | ||| ||     | ||   |   |||  | ||  || |||  | |  | ||  | |  |   || | |  || |   |                                
GTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTTTATCAATCAGGTTTCTCACATGCTTTGAAGgtacattttttgtcctgatt--ctcttgtgaatgaaatcctctaccc--ttcaatgcat-atatatatatttttttaattcttatc-ctgacatgtatctagggga------------------------------

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 5'ss of exon 17
lower sequence: GLYMA01G29470.1 (Glycine max), 5'ss of exon 18
GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtc-ctcttcctaattgattttagtgcattgtcacgtcaggctggttctttacaagatttattcaatcctgtagatatggtgattggcgtaaatttcacgtcgctctaactattcgactctgactgatgcag
||||||||| ||||||| |||||  | ||||| ||||| || ||||| ||||||||||| ||||||   |||     |||||||  |  ||| |||| |||   | | ||| ||     | ||    |    ||  |    |||| || ||| ||     |||  |||    | |   |     | | | |  | |                     
GTGTGGAAGTTGAGCTCATGTGATTTATGTGAGATTGCCCGTAATTCAGTTTATCAATCAGGTTTCTCACATGCTTTAAAGgtacatttctcgtcctgatt--ctcttgtgaatgaaatcctc----tacccctcaatgcaattttttaaattct-----tatcctga----catgtgtccaggggcacccagagt---------------------
















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|162206778|gb|FC383251.1|FC383251
EST:     AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG                         ACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
genomic: AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
EST: gi|162194297|gb|FC369520.1|FC369520
EST:     AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG                         ACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
genomic: AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
EST: gi|19779903|gb|BQ039488.1|BQ039488
EST:     AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG                         ACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
genomic: AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
EST: gi|162268980|gb|FC445472.1|FC445472
EST:     AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG                         ACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
genomic: AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
EST: gi|7147916|gb|AW509838.1|AW509838
EST:     AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG                         ACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
genomic: AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
EST: gi|162206777|gb|FC383250.1|FC383250
EST:     AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG                         ACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
genomic: AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
EST: gi|37852950|gb|BJ610958.1|BJ610958
EST:     AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG                         ACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
genomic: AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
EST: gi|162171487|gb|FC346762.1|FC346762
EST:     AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG                         ACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
genomic: AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
EST: gi|37851047|gb|BJ609055.1|BJ609055
EST:     AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG                         NCACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT
genomic: AAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGAT

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: 8 (upstream exon), 35 (downstream exon)
Score: 5

GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAGgtatgtcctc ... actgatgcagACACATTGGCTGGGGAAAAATTATTACAAGAGGGGTCCTGAGGGGAATGATATTCACAAGACCAATGTTCCTCATATGCGTGTGGAATTCCGTGATGAG




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