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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaagaactttacaccctactgtgggctcatctgcactatgctaaatttcttttaattttgccgtgtgtttgatttttcgcaagcaccagtagttttatgaattcacgagtaagcccttttctgaccgctgcatctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAGATCACCTATTCCAAAGTTCTACATGGCGGGTGACTTCACTAAGCAGAAG

Basic information

species Physcomitrella patens
transcript PP1S369_27V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S369_27V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 12
gtactaagaactttacaccctactgtgggctcatctgcactatgctaaatttcttttaat---tttgccgtgtgtttgatttttcgcaagcaccagtagttttatgaattcacgagtaagcccttttctgaccg-ctgcatc-tttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAGATCACCTATTCCAAAGTTCTACATGGCGGGTGACTTCACTAAGCAGAAG
    |        ||| | |    |  || | || |    || |||   ||| |    ||   ||||   ||| |||| | || |  ||  |  |||    || ||  |||     | |  |||  |   || | || |||  |||||||||||||||||| || || ||| ||||||| |||||| | ||  |||||||||| |||||   |   |||||  | || || || | ||| || || || 
--gtttgattgaatacccacagagggtggattatttctttta-gcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatt-tgtgttc-----tgaatcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA
















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|18337904|gb|BJ169928.1|BJ169928
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|162192388|gb|FC371657.1|FC371657
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|162187987|gb|FC364977.1|FC364977
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|162167173|gb|FC343649.1|FC343649
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|162267103|gb|FC443334.1|FC443334
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|162187988|gb|FC364978.1|FC364978
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|162182136|gb|FC358567.1|FC358567
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|162202347|gb|FC378666.1|FC378666
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|18334431|gb|BJ166448.1|BJ166448
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|37839105|gb|BJ597113.1|BJ597113
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|37846172|gb|BJ604180.1|BJ604180
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|208366040|gb|DC951185.1|DC951185
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|162202823|gb|FC379805.1|FC379805
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|162192389|gb|FC371658.1|FC371658
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
EST: gi|37827985|gb|BJ585997.1|BJ585997
EST:     GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAG                         GTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG
genomic: GACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAG

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: 32 (upstream exon), 33 (downstream exon)
Score: 10

ATGCAACAATGGAAGAGCTAGCCAAATTGTTCCCCAATGAAATTGCAGCTGACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaa ... catctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAGATCACCTATTCCAAAGTTCTACATGGCGGGTGACTTCACTAAGCAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagtagttttatgaattcacgagtaagcccttttctgaccgctgcatctttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAGATCACCTATTCCAAAGTTCTACATGGCGGGTGACTTCACTAAGCAGAAG
                                 ttctgac  putative branch site (score: 10)
                                             catctttc  putative PPT
       ttttatgaatt  TA-rich tract