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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTGCTCGTGCCCGCCGCGCTCTTGAGGCCAAGCGGAAGGGGCGTCACTCTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaactacgatgccgccggtgtgggtttttggatcagtccagttcctgatgttgggtttgggttgcgatcattctgtgttgaaattctcggggagtt...

Basic information

species Physcomitrella patens
transcript PP1S50_102V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S50_102V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv07s0005g00840.t01 (Vitis vinifera), 5'ss of exon 2
--GCGTGCTCGTGCCCGCCGCGCTCTTGAGGCCAAGCGGAAGGGGCGTCACTCTGGTT-ACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaactacgatgccgccggtgtgggtttttggatcagtccagttcctgatgttgggtttgggttgcgatcattctgtgttgaaattctcggggagtt
  |  || |  || |  | |    |        |  |      |   ||   |  ||  |  ||| | | |   |    ||||  | ||  ||    |      |  | | |  ||    ||  |  |  | |||    | ||     |   | || ||| |      ||  |         | ||    || |   | |  |
AAGGATGGTTTTGTCATCAGGAAGCCAACTAAAATTCATTCACGATCTCGTGCACGTCGAATGAAGGAGGCCAAGCGAAAGGGGCGTCACTCTGGATAT-Ggtatttttattttgagtttgcatgcattaggtttcaagtaaggattatattttattttgagaacattttttgggggaataatatttg--tttttatgtatgt
















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|162276186|gb|FC452878.1|FC452878
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|67702082|gb|BJ962315.1|BJ962315
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|22492628|gb|BU052551.1|BU052551
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|67575002|gb|BJ947826.1|BJ947826
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|162213762|gb|FC390377.1|FC390377
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|162219524|gb|FC396482.1|FC396482
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|162278681|gb|FC454791.1|FC454791
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|208374467|gb|DC941196.1|DC941196
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|18339279|gb|BJ171306.1|BJ171306
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|162278682|gb|FC454792.1|FC454792
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|18371469|gb|BJ203071.1|BJ203071
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|67720185|gb|BJ970444.1|BJ970444
EST:     CT-GTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|67698438|gb|BJ958671.1|BJ958671
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|18330842|gb|BJ162848.1|BJ162848
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|162209121|gb|FC385340.1|FC385340
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|162266893|gb|FC443007.1|FC443007
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|37851644|gb|BJ609652.1|BJ609652
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|162209120|gb|FC385339.1|FC385339
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|37829269|gb|BJ587281.1|BJ587281
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|162266892|gb|FC443006.1|FC443006
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|162219525|gb|FC396483.1|FC396483
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|18330981|gb|BJ162987.1|BJ162987
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|7147978|gb|AW509900.1|AW509900
EST:     CCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
EST: gi|67720574|gb|BJ970833.1|BJ970833
EST:     CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAG                         GTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC
genomic: CTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATAC

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), 34 (downstream exon)
Score: 21

GCGTGCTCGTGCCCGCCGCGCTCTTGAGGCCAAGCGGAAGGGGCGTCACTCTGGTTACGGAAAGCGCCGCGGTACCAGGGAAGCCAGACTCCCCACCAAGgtactaacta ... tcgtgtgtagGTTTTGTGGTTGCGGCGAATGCGGGTGTTGAGGCGCCTGCTGCGTAAATACCGTGATGCTAAGAAGATTGACAAGCACATGTACCACGACATGTACATGA




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