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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCCTTCCACAATGTCGGGCCCCGGGTTCTATTACTACAGTGATCCTAGGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgtttttttttttttttttttttttttttttgttggtgtgtgtgtgacgagtggctttcgttgagctttggtgcggagtttcgggcgttcgttcctcggggttgtgttctaggagaggaataatgtgtgtgtgtggattgtgagtttttttggatgattgatcgtgcgttgtgtgcag

Basic information

species Physcomitrella patens
transcript PP1S494_6V6.1
intron # 1
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|208346409|gb|DC912802.1|DC912802
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|18348009|gb|BJ180056.1|BJ180056
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|100356224|gb|BY946257.1|BY946257
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|18352926|gb|BJ184981.1|BJ184981
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|100369626|gb|BY948572.1|BY948572
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|100355300|gb|BY965092.1|BY965092
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|162219181|gb|FC396620.1|FC396620
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|100387241|gb|BY970385.1|BY970385
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|162219180|gb|FC396619.1|FC396619
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|100397749|gb|BY990381.1|BY990381
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|100408559|gb|BY974187.1|BY974187
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|37834364|gb|BJ592376.1|BJ592376
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|7584234|gb|AW700131.1|AW700131
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
EST: gi|100446956|gb|CJ971255.1|CJ971255
EST:     GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTAC                         TGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG
genomic: GGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAG

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: 31 (upstream exon), 35 (downstream exon)
Score: 2

TGCTCCTTCCACAATGTCGGGCCCCGGGTTCTATTACTACAGTGATCCTAGGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgttt ... ttgtgtgcagTGGTTCTATCCTAACAAGGATTTACTCAAGTACCCGATTGAGGAGCCCAAGAAGGACAATAAGAAGGATGACAAGAAGGACGACAAAAAAGACGCTGAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCCTTCCACAATGTCGGGCCCCGGGTTCTATTACTACAGTGATCCTAGGCCCTTTCACAGCTTCCAGCCGCTTCACTCTGATGGATCGCTTGATTACgtaagtgtttttttttttttttttttttttttttttgttggtgtgtgtgtgacgagtggctttcgttgagctttggtgcggagtttcgggcgttcgttcctcggggttgtgttctaggagaggaataatgtgtgtgtgtggattgtgagtttttttggatgattgatcgtgcgttgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA