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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCCGGGTTGTCGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaagaccaaactacattctaagctcctttctgtaccacctcatagcctggaattcaagagtggtgcattcattcaattggtggtccgcaggggaatgtagtaagttttgacgtgcagtaagggttgattgattctgttcacgtacatggtcgatcatatgcag

Basic information

species Physcomitrella patens
transcript PP1S6_148V6.1
intron # 3
splice site 5'
intron type U2

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|18333415|gb|BJ165430.1|BJ165430
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162220971|gb|FC396156.1|FC396156
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162273082|gb|FC447776.1|FC447776
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162190184|gb|FC365926.1|FC365926
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162161863|gb|FC337952.1|FC337952
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAA
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAA
EST: gi|37826992|gb|BJ585004.1|BJ585004
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAAACGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162273081|gb|FC447775.1|FC447775
EST:     CCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|208370955|gb|DC944330.1|DC944330
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|208377435|gb|DC927081.1|DC927081
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|37850462|gb|BJ608470.1|BJ608470
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162190183|gb|FC365925.1|FC365925
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|18335178|gb|BJ167196.1|BJ167196
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162211282|gb|FC387512.1|FC387512
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162220972|gb|FC396157.1|FC396157
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|208351093|gb|DC921339.1|DC921339
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162274451|gb|FC450686.1|FC450686
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|208384841|gb|DC907454.1|DC907454
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|18334705|gb|BJ166722.1|BJ166722
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|208363381|gb|DC946979.1|DC946979
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|162274452|gb|FC450687.1|FC450687
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|208382343|gb|DC919331.1|DC919331
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
EST: gi|100447936|gb|CJ972235.1|CJ972235
EST:     CGCCTGCCATCGTGGGCTCTTTCCCACGCAA-GACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAA
genomic: CGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAA
EST: gi|162211281|gb|FC387511.1|FC387511
EST:     CCACGCAAAGACGCCGCTCTTGTCGAG                         TTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT
genomic: CCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGT

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

AGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCCGGGTTGTCGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaaga ... tcatatgcagTTCTTCATGGATGAGTGCAACCGTCATCTGGAAGACGAAGTTGAAGCCCGTGAGAAAGAGTTGTCCTCCATGCTTCTTGCGGAGCGCATAGCACAGCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGTGGACAGAATCTGCTCTTGTGCAAGGTGCGAAGGACGCCGGGTTGTCGCCTGCCATCGTGGGCTCTTTCCCACGCAAAGACGCCGCTCTTGTCGAGgtaggaaagaccaaactacattctaagctcctttctgtaccacctcatagcctggaattcaagagtggtgcattcattcaattggtggtccgcaggggaatgtagtaagttttgacgtgcagtaagggttgattgattctgttcacgtacatggtcgatcatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG