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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttggggagcggtttatggattttaatttttttgggtgtttttatttacttttgggttttggctgagaagtggttattttttgggcgtgggtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG

Basic information

species Physcomitrella patens
transcript PP1S726_1V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S726_1V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 2
gttggggagcggtttatggattttaatttttttgggtgtttttatttacttttgggtttt--ggctgagaagtggttattttttgggcgtgggtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG
|||          ||       |||  | ||    | ||||||||||  ||||   |||    | | | |      || | |  |  |   | |  | |||| ||||| |||||  |||||||||| || || ||||| || ||||||||||| ||||| || || ||||| |||||||
gtttttctctttctttgttgcgttatctgttaattgcgtttttatttttttttcattttctgagatcaaagtctaataatatacgaacactg-tatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG

upper sequence: PP1S726_1V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ08912 (Selaginella moellendorffii), 3'ss of exon 1
gttggggagcgg---tttatggattttaatttttttgggtgtttttatttacttttgggttttggctgagaagtggttattttttgggcgtgggtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG
||  |  ||||    |  || |  | |  | ||| |      ||  |     ||| ||||| | ||  |      ||    |||   || |       |  |||||| ||||||| || ||||| ||||||||||| || || ||||||||||| ||||| ||| | || || || ||||
gtacgtcagcgcatctccatcgcctctcctctttct-----cttccacagggtttagggttctcgcgcactgacagtctgatttctcgctt-----ctcccagATTTCTGATGAAGCTAAACAACGAGACGGTATCGATCGAGCTCAAGAATGGGACTATTGTGAATGGAACAATCACAG
















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|19778390|gb|BQ039306.1|BQ039306
EST:     TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAG                         ATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGG
genomic: TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAGgtgcggggtc ... gtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGG
EST: gi|19786461|gb|BQ040480.1|BQ040480
EST:     TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAG                         ATTTTTGATGAAACTGAACAATGAGACGGGATCAATAGAACTCAAGAATGG
genomic: TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAGgtgcggggtc ... gtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGG
EST: gi|18327020|gb|BJ159021.1|BJ159021
EST:     TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAG                         ATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGG
genomic: TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAGgtgcggggtc ... gtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGG
EST: gi|19777854|gb|BQ039234.1|BQ039234
EST:     TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAG                         ATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGG
genomic: TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAGgtgcggggtc ... gtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGG
EST: gi|67575738|gb|BJ948562.1|BJ948562
EST:     TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAG                         ATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGG
genomic: TTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAGgtgcggggtc ... gtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGG

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: 25 (upstream exon), 32 (downstream exon)
Score: 11

CTTCTAAGCTACGTTGCATTTCGAAGCTGCAGCCGATTCCTCCTCCGGACTTTGTTTGAGAAGATTCGACAAATTGGGGAGTCACCATGAAGCTTGTCAGgtgcggggtc ... gtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttttgggttttggctgagaagtggttattttttgggcgtgggtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG
                            ttatttttt  TA-rich tract