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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCGGTACAATGTCGGGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtacctcaatttcctgtcgtgggtgaatctagtgtttttctgaaacaccatctgctcaaatgttgggtttggtcgatcagattcctcgtcactt...

Basic information

species Physcomitrella patens
transcript PP1S1_304V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_304V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ26253 (Selaginella moellendorffii), 5'ss of exon 2
GAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCGGTACAATGTCGGGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtacctcaatttcctgtcg-tgggtgaatctagtgtttttctgaaacaccatctgctcaaatgttgggtttggtcgatcagattcctcgtcactt
 ||||| ||  | |||||||| || || ||||| || || ||| || || | ||    || ||||| ||||||||||| || |||||||||||||| ||||| ||  |   | |    |   ||| ||| |   |  |  |   |     |||    |   ||   || |  || |  |                      
AAACGGCAGGCTCAACAAGTGTGGAGTCATCAGCCCGCGCTACGATATCAGCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatt--ttgagagacgaatcgatggcttggtgcaaagaact-----aacgattttctcttcgatctctggctcag----------------------

upper sequence: PP1S1_304V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ14550 (Selaginella moellendorffii), 5'ss of exon 2
GAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCGGTACAATGTCGGGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtacctcaatttcctgtcgtgggtgaatctagtgtttttctgaaacaccatctgctcaaatgttgggtttggtcgatcagattcctcgtcactt
 ||||| ||  | |||||||| || || ||||| || || ||| || || | ||    || ||||| ||||||||||| || |||||||||||||| ||||| ||  |   | |    |   |||  ||      | |||       | |||    |   ||   || |  || |  |                      
AAACGGCAGGCTCAACAAGTGTGGAGTCATCAGCCCGCGCTACGATATCAGCGTCAAGGAGCTCGAGGCCTGGACTGCTCGGCTTCTTCCATCTCGCCAGgtttgatt--ttgagagacgaatcgatggc----ttggtgcaaagaagtaacgattttctcttcgatctctggctcag----------------------
















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|162218720|gb|FC394270.1|FC394270
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|18373221|gb|BJ204823.1|BJ204823
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|18356753|gb|BJ188812.1|BJ188812
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|67576889|gb|BJ949713.1|BJ949713
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|67698027|gb|BJ958260.1|BJ958260
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|162226357|gb|FC403273.1|FC403273
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|162273654|gb|FC449383.1|FC449383
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|67573039|gb|BJ945863.1|BJ945863
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|37843743|gb|BJ601751.1|BJ601751
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|37833696|gb|BJ591708.1|BJ591708
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|162273653|gb|FC449382.1|FC449382
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|162202882|gb|FC379864.1|FC379864
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|162194896|gb|FC370547.1|FC370547
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|67700425|gb|BJ960658.1|BJ960658
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|67696421|gb|BJ956654.1|BJ956654
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|162218719|gb|FC394269.1|FC394269
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|162269511|gb|FC445067.1|FC445067
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|162226443|gb|FC402423.1|FC402423
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|162202881|gb|FC379863.1|FC379863
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
EST: gi|67574609|gb|BJ947433.1|BJ947433
EST:     GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAG                         TTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG
genomic: GGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAG

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: 33 (upstream exon), 35 (downstream exon)
Score: 59

GAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCGGTACAATGTCGGGGTTGGTGAACTCGAAGCCTGGACTGCCCGACTTCTTCCATCTCGTCAGgtatgtgtac ... ttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAGGCTAGAAGGAAGAATGTTGGAGGAAAGGTCCTTGGTTTCTTTTACTGAG




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