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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcgtctcctaaagggggtcgttggaatcggtttcacaccactattagagctttttgtcattttacatgctgcatctctgcttcttgattactcgcagtttagttattggcgtaaattttgctgttgatgtaagtttttaagtatgtctttttgttgaaatttgttcgtttttgtgatgaaatgcagGTGGGGTTCAACATGCGCAAGGTGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATT

Basic information

species Physcomitrella patens
transcript PP1S103_13V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S103_13V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgtcgtctcctaaagggggtcgttggaatcggtttcacaccactattagagctttttgtcattttacatgctgcatctctgcttcttgattactcgcagtttagttattggcgtaaattttgctgttgatgtaagtttttaagtatgtctttttgttgaaatttgttcgtttttgtgatgaaatgcagGTGGGGTTCAACATGCGCAAGGTGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATT
                                                                                                            | ||    ||  ||| | ||  || |||  |  ||     ||   |  |  | |||    |   |  |  |  |       |||| || ||||||||| | || ||||| || || ||||| || ||||| || |||||||||||||| |||||  | ||||| ||||||||||| ||||| |
---------------------------------------------------------------------------------------------------------gtgtgttatactacttttaggtggcgaagtatttgcttgctcttggactaatcgtaaaaaggatgtttactctttct------tagGTTGGTTTCAACATGAGGAAAGTGACAAAAGGAAGTGTCACGATCAAGCTTTGGGATCTCGGTGGTCAACCTAGGTTCCGCAGCATGTGGGAACGTTACT

upper sequence: PP1S103_13V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G49870.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgtcgtctcctaaagggggtcgttggaatcggtttcacaccactattagagctttttgtcattttacatgctgcatctctgcttcttgattactcgcagtttagttattggcgtaaattttgctgttgatgtaagtttttaagtatgtctttttgttgaaatttgttcgtttttgtgatgaaatgcagGTGGGGTTCAACATGCGCAAGGTGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATT
                                                                                            | |     |   ||  | |     |||| ||     || |  ||| || |  | ||   | |   |    |  |  || || ||| ||||      ||||| ||||| |||||| | || || || || || | ||| || |||||||| |||||||| ||||| |||||  ||||||| ||||||||||| ||||| |
-------------------------------------------------------------------------------------------gtaagcgttacactacatgtct-tataaagttcatctttcacctaacttgtggaataa--catgaagagatatctcctttgtgtttttgat------cagGTCGGGTTTAACATGAGGAAAGTAACAAAAGGAAATGTTACAATCAAACTATGGGATCTTGGTGGTCAACCAAGATTCCGCAGCATGTGGGAACGTTACT

upper sequence: PP1S103_13V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ07633 (Selaginella moellendorffii), 3'ss of exon 3
gtacgtcgtctcctaaagggggtcgttggaatcggtttcacaccactattagagctttttgtcattttacatgctgcatctctgcttcttgattactcgcagtttagttattggcgtaaattttgctgttgatgtaagtttttaagtatgtctttttgttgaaatttgttcgtttttgtgatgaaatgcagGTGGGGTTCAACATGCGCAAGGTGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATT
                                                                                                                   |||    || || | |||  |    |    || |      |   |||  |  |    | | | |        ||||||||| ||||||||| | || ||||| || || | |||||| ||||| || |||||||| || || ||||| || |||||||| ||||||||||| ||||
-------------------------------------------------------------------------------------------------------------------gtaggaatt-ctctcgatcgatccatccttgtctcctccatgcctgacctgaggatctctctct-------cgcagGTGGGATTCAACATGAGAAAAGTGACCAAAGGCAATGTGACGATCAAGCTGTGGGATCTGGGCGGACAACCACGCTTCCGGAGTATGTGGGAGCGCTATT

upper sequence: PP1S103_13V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ11035 (Selaginella moellendorffii), 3'ss of exon 3
gtacgtcgtctcctaaagggggtcgttggaatcggtttcacaccactattagagctttttgtcattttacatgctgcatctctgcttcttgattactcgcagtttagttattggcgtaaattttgctgttgatgtaagtttttaagtatgtctttttgttgaaatttgttcgtttttgtgatgaaatgcagGTGGGGTTCAACATGCGCAAGGTGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATT
                                                                                                                   |||    || |||| |||          |   ||   ||| |  |  |   ||   |   |   |||     ||||||||| ||||||||| | || ||||| || || | |||||| ||||| || |||||||| || || ||||| || |||||||| ||||||||||| ||||
-------------------------------------------------------------------------------------------------------------------gtaggaatt-ctgtcgat--------cgatccatccttttctcctcca---tgcctgacctgaggatctctcgcagGTGGGATTCAACATGAGAAAAGTGACCAAAGGCAATGTGACGATCAAGCTGTGGGATCTGGGCGGACAACCACGCTTCCGGAGTATGTGGGAGCGCTATT

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|100354463|gb|BY983432.1|BY983432
EST:     ACGGGTAGCTTTGCTGAGGACATGATACCCACG                         GTGGGGTTCAACATGCGCAAGGTGGAC-AAGGGTAGTGTGACCTTTCAA-C
genomic: ACGGGTAGCTTTGCTGAGGACATGATACCCACGgtacgtcgtc ... tgaaatgcagGTGGGGTTCAACATGCGCAAGGTG-ACGAAGGGTAGTGTGAC-TATCAAAC
EST: gi|100383532|gb|BY950316.1|BY950316
EST:     ACGGGTAGCTTTGCTGAGGACATGATACCCACG                         GTGGGGTTCAACATGC
genomic: ACGGGTAGCTTTGCTGAGGACATGATACCCACGgtacgtcgtc ... tgaaatgcagGTGGGGTTCAACATGC
EST: gi|100422708|gb|BY957961.1|BY957961
EST:     ACGGGTAGCTTTGCTGAGGACATGATACCCACG                         GTGGGGTTCAACATGCGC
genomic: ACGGGTAGCTTTGCTGAGGACATGATACCCACGgtacgtcgtc ... tgaaatgcagGTGGGGTTCAACATGCGC

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), 30 (downstream exon)
Score: 10

ACGGGTAGCTTTGCTGAGGACATGATACCCACGgtacgtcgtc ... tgaaatgcagGTGGGGTTCAACATGCGCAAGGTGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttaagtatgtctttttgttgaaatttgttcgtttttgtgatgaaatgcagGTGGGGTTCAACATGCGCAAGGTGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATT
                tttttgttgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtcgtctcctaaagggggtcgttggaatcggtttcacaccactattagagctttttgtcattttacatgctgcatctctgcttcttgattactcgcagtttagttattggcgtaaattttgctgttgatgtaagtttttaagtatgtctttttgttgaaatttgttcgtttttgtgatgaaatgcagGTGGGGTTCAACATGCGCAAGGTGACGAAGGGTAGTGTGACTATCAAACTCTGGGATCTCGGTGGCCAACCCCGATTCCGGAGCATGTGGGAGCGTTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA