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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttcatcctaccccaggatcaagtactttgcaatatattattgctgttgcgtaggaacgggtttcaagcgcatgatggtggtggtattggggctaggaggtggtgttctaatgtggctctgcgatttggtgaaattgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCCCCACTGACCGATGACCAGATTGCTAAGCAGGTGGACTACATGATCCAGC

Basic information

species Physcomitrella patens
transcript PP1S204_96V6.1
intron # 1
splice site 3'
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|162241768|gb|FC417295.1|FC417295
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162231518|gb|FC407968.1|FC407968
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162208604|gb|FC384793.1|FC384793
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162251312|gb|FC425510.1|FC425510
EST:     TTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAC                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: TTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162230886|gb|FC406725.1|FC406725
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162211326|gb|FC387556.1|FC387556
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162248797|gb|FC422843.1|FC422843
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162226620|gb|FC402717.1|FC402717
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162240443|gb|FC414371.1|FC414371
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162188994|gb|FC364384.1|FC364384
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162248798|gb|FC422844.1|FC422844
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162241769|gb|FC417296.1|FC417296
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162272542|gb|FC447700.1|FC447700
EST:     CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162243262|gb|FC415614.1|FC415614
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162231517|gb|FC407967.1|FC407967
EST:     CTCAGAAG-TGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162202307|gb|FC378652.1|FC378652
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162251539|gb|FC425581.1|FC425581
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162226619|gb|FC402716.1|FC402716
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162211327|gb|FC387557.1|FC387557
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162208693|gb|FC384829.1|FC384829
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162234706|gb|FC410452.1|FC410452
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162210957|gb|FC387055.1|FC387055
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162243263|gb|FC415615.1|FC415615
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162224407|gb|FC399588.1|FC399588
EST:     GTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: GTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162239558|gb|FC414071.1|FC414071
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162206669|gb|FC382427.1|FC382427
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162280346|gb|FC456051.1|FC456051
EST:     CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACCTTGCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTA-CTTGCC
EST: gi|162248163|gb|FC419713.1|FC419713
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162258915|gb|FC435858.1|FC435858
EST:     CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162248164|gb|FC419714.1|FC419714
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162230163|gb|FC406311.1|FC406311
EST:     CTCAGAAGTTGGGAGCCGTCCAAAATGGCAGCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: CTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
EST: gi|162226083|gb|FC401036.1|FC401036
EST:     GCCGCGTGCAATGCATGCAG                         GTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC
genomic: GCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCC

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), 35 (downstream exon)
Score: 1315

CGTCAAGGCTTTCTCTGGCCTGAAGCCGGCTACCCTGTTCTCCAGCAAGACTCAGAAGTTGGGAGCCGTCCAGAATGGCAGCCGCGTGCAATGCATGCAGgtgtgttcat ... ttgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCCCCACTGACCGATGACCAGATTGCTAAGCAGGTGGACTACATGATCCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggctaggaggtggtgttctaatgtggctctgcgatttggtgaaattgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCCCCACTGACCGATGACCAGATTGCTAAGCAGGTGGACTACATGATCCAGC
                ttctaat  putative branch site (score: 1315)
                ttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttcatcctaccccaggatcaagtactttgcaatatattattgctgttgcgtaggaacgggtttcaagcgcatgatggtggtggtattggggctaggaggtggtgttctaatgtggctctgcgatttggtgaaattgtgctcagGTGTGGAACCCGATCGGACAGCCCAAGTTCGAGACCTTCTCGTACTTGCCCCCACTGACCGATGACCAGATTGCTAAGCAGGTGGACTACATGATCCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA