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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattagcctattaccaaaaaaattcgaatgtccagcagggttggcgatgaagttgaagggttaaattcacttcaaatctattggtgaccatttctggatcatgtgtgttaagtagtttgatctttctgtacgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG

Basic information

species Physcomitrella patens
transcript PP1S100_23V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_23V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ09736 (Selaginella moellendorffii), 3'ss of exon 11
gtattagcctattaccaaaaaaattcgaatgtccagcagggttggcgatgaagttgaagggttaaattcacttcaaatctattggtgaccatttctggatcatgtgtgttaagtagtttgatctttctgtacgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG
                                                                             |             | ||  ||  | |  ||||  |    |    | |  |   | | |  ||||||||||| ||||| || ||||| ||||| |||||||||||||| ||| | ||||| |||   || || ||||||
----------------------------------------------------------------------------gtgatgctccatttctctccagaaaaaggatgtt--gctaatcatccatctttggcttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCCATGTACACCCGCATAACCGGAAAG

upper sequence: PP1S100_23V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ11673 (Selaginella moellendorffii), 3'ss of exon 11
gtattagcctattaccaaaaaaattcgaatgtccagcagggttggcgatgaagttgaagggttaaattcacttcaaatctattggtgaccatttctggatcatgtgtgttaagtagtttgatctttctgtacgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG
                                                                             |             | ||  ||  | |  ||||  |    |    | |  |   | | |  ||||||||||| ||||| || ||||| ||||| |||||||||||||| ||| | ||||| |||   || || ||||||
----------------------------------------------------------------------------gtgatgctccatttctctccagaaaaaggatgtt--gctaatcatccatcgttggcttttttcagAGCTACGACCCAACCACACACTTTGAGACTACAGTGCAAGATGTTCTTGCCATGTACACCCGCATAACCGGAAAG
















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|37840302|gb|BJ598310.1|BJ598310
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|208373324|gb|DC944967.1|DC944967
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|162159099|gb|FC334270.1|FC334270
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|208372810|gb|DC956211.1|DC956211
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|67698955|gb|BJ959188.1|BJ959188
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|37837357|gb|BJ595365.1|BJ595365
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|18335062|gb|BJ167080.1|BJ167080
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|162225721|gb|FC401863.1|FC401863
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|37847853|gb|BJ605861.1|BJ605861
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|208371608|gb|DC952250.1|DC952250
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|162159100|gb|FC334271.1|FC334271
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
EST: gi|37852235|gb|BJ610243.1|BJ610243
EST:     TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAG                         AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA
genomic: TGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCA

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: 32 (upstream exon), 33 (downstream exon)
Score: 3

GCTTGCACTCCTTGGAAAAATTGATGAGAAGATTATTGACATGTATGACATGTACGAGCCAGTCAATGATTCTTCACTTGACAACTGCTTCATTTCGAAGgtattagcct ... cgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccatttctggatcatgtgtgttaagtagtttgatctttctgtacgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG
                             gtttgat  putative branch site (score: 3)
                      ttaagta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattagcctattaccaaaaaaattcgaatgtccagcagggttggcgatgaagttgaagggttaaattcacttcaaatctattggtgaccatttctggatcatgtgtgttaagtagtttgatctttctgtacgtgtggcagAGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG