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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGAACGGTACCCTTGTGAGAGTTCTCATTCACACGGATGTGACAAAATATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactcgtctttcttgttcaagaacgttacattagtagtgtgaagtaccggtaaattatcaagtcattcttagatagatgcgttttgttcctatct...

Basic information

species Physcomitrella patens
transcript PP1S100_23V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 4
GGCGAACGGTACCCTTGTGAGAGTTCTCATTCACACGGATGTGACAAAATATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtg------tgcactcgtctttcttgttcaagaacgttacatt---agtagtgtgaagtaccggtaaattatcaagtcattcttagatagatgcgtt-ttgttcctatct--------------------------------
||| || || ||  | || ||    || |||||||| ||||||||||| ||||| |  || || ||||||||||| |||||||||| ||   |||| |||||       |   ||  | ||  |  || || | | | | |||     ||||||    |    ||   || | |  ||  | ||     |||  ||| || |||||||                                  
GGCAAATGGCACATTGGTAAGGACCCTGATTCACACTGATGTGACAAAGTATTTGTCATTCAAAGCTGTTGATGGGAGCTACGTCTTCAGCAAAGGGAAGgtaacatcttcagcttatgttagtcttttaatagcatcatatttccgatagtgttttctctaagtgg-ttgttagatctatattctggtgatctgttcttattcctattaacatacccttttctattttcattgtcaatcag

upper sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 4
GGCGAACGGTACCCTTGTGAGAGTTCTCATTCACACGGATGTGACAAAATATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtg------tgcactcgtctttcttgt--tcaagaacgttacattagtagtgtgaagtaccggtaaattatc-aagtcattcttagatagatgc----gttttgttcctatct------------------------------------------
||| || || || || || ||    ||||||||||| ||||||||||| ||||| |  || || ||||| ||||||||||| |||| ||   |||| |||||       |   ||| | |    |||  |||  | | | |||||  |  | |   ||         ||||| ||||  || || |||  ||       | || |||||||                                            
GGCAAATGGGACACTGGTTAGGACCCTCATTCACACTGATGTGACAAAGTATTTGTCATTCAAAGCTGTCGATGGAAGCTATGTCTTCAGCAAAGGGAAGgtaacatcttcagctcatttcctctgttttcattagcatcacatt--tcctctagtgttttatacttttatctaagtggttgttggatctatattctgatcttattcctatgctagcagtgtaacatgcacttttctatttttgctgtcaaccag
















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|67577912|gb|BJ950079.1|BJ950079
EST:     ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAG                         GTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
genomic: ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
EST: gi|208358392|gb|DC943223.1|DC943223
EST:     ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAG                         GTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
genomic: ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
EST: gi|18363088|gb|BJ195160.1|BJ195160
EST:     ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAG                         GTTTACAAGGTTCCATCAAATGACGTGGAGGCACTTGAAGTCTCCTTTGAT
genomic: ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACT-GAAGTCTCCTTTGAT
EST: gi|18372716|gb|BJ204318.1|BJ204318
EST:     ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAG                         GTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
genomic: ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
EST: gi|18367371|gb|BJ199454.1|BJ199454
EST:     ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAG                         GTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
genomic: ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
EST: gi|18331573|gb|BJ163584.1|BJ163584
EST:     ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAG                         GTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
genomic: ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
EST: gi|100437761|gb|BY979815.1|BY979815
EST:     ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAG                         GTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
genomic: ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
EST: gi|18357992|gb|BJ190051.1|BJ190051
EST:     ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAG                         GTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
genomic: ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
EST: gi|208359106|gb|DC930438.1|DC930438
EST:     ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAG                         GTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
genomic: ATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATG
EST: gi|100442258|gb|BY981282.1|BY981282
EST:     TTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACNATCAAGGAAAAG                         GTT-ACAAGGGTCCATCAAATGACGTGGAGGCCCTGAGGTCTCCTTTGAT
genomic: TTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAA-Ggtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGAT

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: 30 (upstream exon), 26 (downstream exon)
Score: 7

GGCGAACGGTACCCTTGTGAGAGTTCTCATTCACACGGATGTGACAAAATATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactc ... atgtttatagGTTTACAAGGTTCCATCAAATGACGTGGAGGCACTGAAGTCTCCTTTGATGGGACTATTTGAAAAGAGGCGTGCCCGCAAATTTTTTATCTTTGTCCAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGAACGGTACCCTTGTGAGAGTTCTCATTCACACGGATGTGACAAAATATTTATTGTTTAAGGCTGTTGATGGAAGCTACGTCTACAATCAAGGAAAGgtgtgcactcgtctttcttgttcaagaacgttacattagtagtgtgaagtaccggtaaattatcaagtcattcttagatagatgcgttttgttcctatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA