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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAGGGCCTCATGAAGTTGATGGAAGGTGAACATGTTGGGCCTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtatttttatggcctttgcagttgccgccgtgcattgtaatttctgaccatgattagtgagtctcttgttgtggaacgttttatttatttatttat...

Basic information

species Physcomitrella patens
transcript PP1S120_29V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S120_29V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 5'ss of exon 6
GTGGAGGGCCTCATGAAGTTGATGGAAGGTGAACATGTTGGGCCTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtatttttatggcctttgcagttgccgccgtgcattgtaatttctgaccatgattagtgagtctcttgttgtggaacgttttatttatttatttat-------------------
|| || ||  | || |   |||||||| |||| ||| | || |||||||| |||||||||||||| ||||| |||||| | || || || |||||  |     | ||  | |         |   | |||| |     |    || ||| || | |    |      |        ||| |  |   | | ||                   
GTTGATGGATTGATAACCCTGATGGAAAGTGAGCATATAGGACCTTTCAACTTGGGAAATCCTGGAGAATTTACCATGTTAGAGCTTGCTCAGgttcg-gccctcata-cttcaaatccaactatcctgcaatccttgtatgaacaatgctttgggttcttgcctgggctttctactttctacaagcaatcatgtgcctgctacttctgtag
















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|37845110|gb|BJ603118.1|BJ603118
EST:     CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAG                         GTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
genomic: CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtattt ... tgtgttacagGTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
EST: gi|37840587|gb|BJ598595.1|BJ598595
EST:     GAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAG                         GTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
genomic: GAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtattt ... tgtgttacagGTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
EST: gi|162239440|gb|FC414031.1|FC414031
EST:     CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAG                         GTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
genomic: CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtattt ... tgtgttacagGTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
EST: gi|37852025|gb|BJ610033.1|BJ610033
EST:     CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAA                         GTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
genomic: CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtattt ... tgtgttacagGTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
EST: gi|162176699|gb|FC352544.1|FC352544
EST:     CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAG                         GTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
genomic: CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtattt ... tgtgttacagGTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
EST: gi|37837693|gb|BJ595701.1|BJ595701
EST:     CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAG                         GTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
genomic: CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtattt ... tgtgttacagGTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
EST: gi|37846830|gb|BJ604838.1|BJ604838
EST:     CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAA                         GTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
genomic: CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtattt ... tgtgttacagGTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
EST: gi|37851574|gb|BJ609582.1|BJ609582
EST:     CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAG                         GTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC
genomic: CTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtattt ... tgtgttacagGTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAAC

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: 15 (upstream exon), 32 (downstream exon)
Score: 4

GTGGAGGGCCTCATGAAGTTGATGGAAGGTGAACATGTTGGGCCTTTCAATTTGGGAAATCCTGGCGAATTCACCATGCTTGAACTCGCACAGgtgagtattt ... tgtgttacagGTGGTTAAGGATGTGATCGACCCTACCGCGACGATTGAATACAAAGAGAACACATCCGATGACCCACACAAGCGCAAGCCTGATATCTCCAAGGCCAAGG




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