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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttattattgggtgagaagtccctcttttgtccgtttaacccgttggataattaaaaagcgtataaatgtgtatcaattggtttgatggtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTGCAGGCAGCTTCTGGGGTCACA

Basic information

species Physcomitrella patens
transcript PP1S78_27V6.1
intron # 2
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|100392454|gb|BY953371.1|BY953371
EST:     GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAG                         GAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
genomic: GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAGgtatgcgatt ... gtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
EST: gi|18370158|gb|BJ201760.1|BJ201760
EST:     GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAG                         GAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
genomic: GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAGgtatgcgatt ... gtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
EST: gi|18374378|gb|BJ205956.1|BJ205956
EST:     GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAG                         GAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
genomic: GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAGgtatgcgatt ... gtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
EST: gi|18373692|gb|BJ205270.1|BJ205270
EST:     GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAG                         GAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
genomic: GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAGgtatgcgatt ... gtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
EST: gi|18348835|gb|BJ180884.1|BJ180884
EST:     GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAG                         GAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
genomic: GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAGgtatgcgatt ... gtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
EST: gi|100442322|gb|BY981346.1|BY981346
EST:     GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAG                         GAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
genomic: GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAGgtatgcgatt ... gtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
EST: gi|18365061|gb|BJ197135.1|BJ197135
EST:     GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAG                         GAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
genomic: GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAGgtatgcgatt ... gtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
EST: gi|100373686|gb|BY967780.1|BY967780
EST:     GGCGTATGGACAGGCTCATCCGACTCCGTCTCCTAGTGGATCCGGAAGAG                         GAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG
genomic: GGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAGgtatgcgatt ... gtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTG

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: 48

GGTAATCCATATGCCCACTATGACAATCAAGGGGTGCCTGGAGGCGCTGCGGCGTATGGACAGGCTCATCCGACTTCGTCTCCTAGTGGATCCGGAAGAGgtatgcgatt ... gtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTGCAGGCAGCTTCTGGGGTCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggataattaaaaagcgtataaatgtgtatcaattggtttgatggtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTGCAGGCAGCTTCTGGGGTCACA
                                     gtttgat  putative branch site (score: 48)
     taattaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttattattgggtgagaagtccctcttttgtccgtttaacccgttggataattaaaaagcgtataaatgtgtatcaattggtttgatggtatactcagGAGGTGCTATGGAATATTTGAACAAGTGGGGAAAACAGGCCGAGAGTATTGCAGGCAGCTTCTGGGGTCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT