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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcacacatccttgccttgtctacttgttcctggcagtgtttaatggtgatgcttagttgttacagctggacagtattttctctgtgattctagaggttctggtacttcagtaagacttaatagtatcatgatgacacttattgtgcaggtagTTGGAGCGGCACCATGAATGCTTCCAAACTCCTCAAGGCTGTTCTACGGCCGCGGTCCATTCAGACCAATAGTGGCAGGGGGCCCGCTGTTTCAGATGGA

Basic information

species Physcomitrella patens
transcript PP1S93_140V6.1
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|208384890|gb|DC907503.1|DC907503
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|208384890|gb|DC907503.1|DC907503
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100406911|gb|BY973928.1|BY973928
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100406911|gb|BY973928.1|BY973928
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100363606|gb|BY966471.1|BY966471
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100363606|gb|BY966471.1|BY966471
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18372321|gb|BJ203923.1|BJ203923
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18372321|gb|BJ203923.1|BJ203923
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18353883|gb|BJ185938.1|BJ185938
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18353883|gb|BJ185938.1|BJ185938
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100403631|gb|BY955023.1|BY955023
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100403631|gb|BY955023.1|BY955023
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18343366|gb|BJ175404.1|BJ175404
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18343366|gb|BJ175404.1|BJ175404
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100353149|gb|BY945630.1|BY945630
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100353149|gb|BY945630.1|BY945630
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100446311|gb|CJ970610.1|CJ970610
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGGTAG                      
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCC---T-Ggtaggcacac ... gtgcagg
EST: gi|100407667|gb|BY991795.1|BY991795
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100407667|gb|BY991795.1|BY991795
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100365360|gb|BY966559.1|BY966559
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100365360|gb|BY966559.1|BY966559
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18372252|gb|BJ203854.1|BJ203854
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18372252|gb|BJ203854.1|BJ203854
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100443115|gb|BY981741.1|BY981741
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100443115|gb|BY981741.1|BY981741
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100380408|gb|BY986685.1|BY986685
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100380408|gb|BY986685.1|BY986685
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|208360369|gb|DC930764.1|DC930764
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|208360369|gb|DC930764.1|DC930764
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18342966|gb|BJ175002.1|BJ175002
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         TTGGAGCGGCACCATGAATGCTTCCAAACTCCTCAAGGCTGTTCTACGGCC
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtagTTGGAGCGGCACCATGAATGCTTCCAAACTCCTCAAGGCTGTTCTACGGCC
EST: gi|100398467|gb|BY972620.1|BY972620
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100398467|gb|BY972620.1|BY972620
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|67716917|gb|BJ967176.1|BJ967176
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|67716917|gb|BJ967176.1|BJ967176
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100443063|gb|BY981689.1|BY981689
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100443063|gb|BY981689.1|BY981689
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100383779|gb|BY969308.1|BY969308
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100383779|gb|BY969308.1|BY969308
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100445618|gb|CJ969917.1|CJ969917
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100445618|gb|CJ969917.1|CJ969917
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18347815|gb|BJ179862.1|BJ179862
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|18347815|gb|BJ179862.1|BJ179862
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|208363756|gb|DC931080.1|DC931080
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|208363756|gb|DC931080.1|DC931080
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100446148|gb|CJ970447.1|CJ970447
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100446148|gb|CJ970447.1|CJ970447
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100450356|gb|CJ974222.1|CJ974222
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-
EST: gi|100450356|gb|CJ974222.1|CJ974222
EST:     CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTG                         G
genomic: CCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtag-

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: 26 (upstream exon), 22 (downstream exon)
Score: 6

GTAATTTTACGGACATGGAGCACCATTTGGACCTGACAGTCACTTGAGTTCCTCTCGACGCATTTGAGCTCCGTTTGGTATCACCTTTGTTTCTTGCCTGgtaggcacac ... gtgcaggtagTTGGAGCGGCACCATGAATGCTTCCAAACTCCTCAAGGCTGTTCTACGGCCGCGGTCCATTCAGACCAATAGTGGCAGGGGGCCCGCTGTTTCAGATGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggtacttcagtaagacttaatagtatcatgatgacacttattgtgcaggtagTTGGAGCGGCACCATGAATGCTTCCAAACTCCTCAAGGCTGTTCTACGGCCGCGGTCCATTCAGACCAATAGTGGCAGGGGGCCCGCTGTTTCAGATGGA
                 acttaat  putative branch site (score: 6)
                   ttaatagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcacacatccttgccttgtctacttgttcctggcagtgtttaatggtgatgcttagttgttacagctggacagtattttctctgtgattctagaggttctggtacttcagtaagacttaatagtatcatgatgacacttattgtgcaggtagTTGGAGCGGCACCATGAATGCTTCCAAACTCCTCAAGGCTGTTCTACGGCCGCGGTCCATTCAGACCAATAGTGGCAGGGGGCCCGCTGTTTCAGATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA