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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCAAGCAAAAGAACTTCAGGATCATCTGGATAGTGTGCTTGCAAATCAACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAGgtaaagttctgtgcatcactttttttctagcatgatgtgcaatgatgtcccgatcaattctaatttcgtatgtgggaccgagcag

Basic information

species Physcomitrella patens
transcript PP1S81_200V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S81_200V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA20G25540.2 (Glycine max), 5'ss of exon 3
GTGGCAAGCAAAAGAACTTCAGGATCATCTGGATAGTGTGCTTGCAAATCAACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAGgt-----aaagttctgtgcatcactttttttctagcatgatgt--gcaatgatgtcccgatcaattcta-atttcgtatgtgggaccgagcag-------
 || ||||| ||||| |||   ||||||||||| ||||| ||||| ||| | || || |||||||||||| |  |  ||||||| |||||||||||||||||     ||||          |||||||| ||||   | | ||  |  ||  |  |  ||  || | || | ||  ||||        ||          
ATGCCAAGCTAAAGAGCTTTTTGATCATCTGGAAAGTGTTCTTGCCAATGAGCCTGTTTCTGTTAAGAGTAGTCCAAACATTGTGGAAGTAAAACCTCAGgtcagtaaaagaaaaactttccactttttatctatttttaggttagtcatatttgcttgaagaagtttatactttatatgcatcttatagacatgacttg
















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|37852219|gb|BJ610227.1|BJ610227
EST:     AACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAG                         GGCGTGAGTAAAGGGGTGGTTGTGGAAGAACTACTGGCGATGATGGCTCTG
genomic: AACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAGgtaaagttct ... gaccgagcagGGCGTGAGTAAAGGGGTGGTTGTGGAAGAACTACTGGCGATGATGGCTCTG
EST: gi|37849393|gb|BJ607401.1|BJ607401
EST:     AACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAG                         GGCGTGAGTAAAGGGGTGGTTGTGGAAGAACTACTGGCGATGATGGCTCTG
genomic: AACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAGgtaaagttct ... gaccgagcagGGCGTGAGTAAAGGGGTGGTTGTGGAAGAACTACTGGCGATGATGGCTCTG
EST: gi|37830621|gb|BJ588633.1|BJ588633
EST:     AACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAG                         GGCGTGAGTAAAGGGGTGGTTGTGGAAGAACTACTGGCGATGATGGCTCTG
genomic: AACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAGgtaaagttct ... gaccgagcagGGCGTGAGTAAAGGGGTGGTTGTGGAAGAACTACTGGCGATGATGGCTCTG
EST: gi|37831838|gb|BJ589850.1|BJ589850
EST:     AACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAG                         GGCGTGAGTAAAGGGGTGGTTGTGGAAGAACTACTGGCGATGATGGCTCTG
genomic: AACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAGgtaaagttct ... gaccgagcagGGCGTGAGTAAAGGGGTGGTTGTGGAAGAACTACTGGCGATGATGGCTCTG

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: 34 (upstream exon), 27 (downstream exon)
Score: 17

GTGGCAAGCAAAAGAACTTCAGGATCATCTGGATAGTGTGCTTGCAAATCAACCCGTGTCTGTTAAGAGTGGGGCGCACATTGTCGAAGTAAAACCTCAGgtaaagttct ... gaccgagcagGGCGTGAGTAAAGGGGTGGTTGTGGAAGAACTACTGGCGATGATGGCTCTGAAGAGTGCTGCTCCAGATTTTGTGCTGTGTATTGGTGATGACCGATCTG




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