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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGACACTATTTGTTGAGGACAATCAAGGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcatactcaacattttcttccaatggtgtacaaaagactagtatggaaatagttatgattgggagctgattggtttgaaatatggctttaatgtgcag

Basic information

species Physcomitrella patens
transcript PP1S41_70V6.1
intron # 7
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|18334808|gb|BJ166825.1|BJ166825
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|208372651|gb|DC944630.1|DC944630
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|208353940|gb|DC930094.1|DC930094
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|162241394|gb|FC418559.1|FC418559
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|162244584|gb|FC423446.1|FC423446
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|67721131|gb|BJ971390.1|BJ971390
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|162184696|gb|FC361934.1|FC361934
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|7148048|gb|AW509970.1|AW509970
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAACGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|19780510|gb|BQ039570.1|BQ039570
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|37831031|gb|BJ589043.1|BJ589043
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|67720438|gb|BJ970697.1|BJ970697
EST:     GGAGGAGGNGAAGTAACCCAGCTTCAGAANCTCGCTATTGTTGGTAGCAC                         GGTNGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAANCGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|67709266|gb|BJ965082.1|BJ965082
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|162244583|gb|FC423445.1|FC423445
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
EST: gi|162241395|gb|FC418560.1|FC418560
EST:     GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCAC                         GGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG
genomic: GGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGG

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), 31 (downstream exon)
Score: 15

TTTGACACTATTTGTTGAGGACAATCAAGGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcat ... taatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGGATGAGACCCTAGCTGGTGCGTCTTAAGTTGTCTTTGGTCATTGATGTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGACACTATTTGTTGAGGACAATCAAGGAGGAGGCGAAGTAACCCAGCTTCAGAAACTCGCTATTGTTGGTAGCACgtaagttcatactcaacattttcttccaatggtgtacaaaagactagtatggaaatagttatgattgggagctgattggtttgaaatatggctttaatgtgcag

- - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - -  GAGGAG