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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcatactcaacattttcttccaatggtgtacaaaagactagtatggaaatagttatgattgggagctgattggtttgaaatatggctttaatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGGATGAGACCCTAGCTGGTGCGTCTTAAGTTGTCTTTGGTCATTGATGTCA

Basic information

species Physcomitrella patens
transcript PP1S41_70V6.1
intron # 7
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|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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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaatagttatgattgggagctgattggtttgaaatatggctttaatgtgcagGGTCGAAACTACAAACATGAAGGATTTGAAGAAGATCAGTGAAAACGAAGGATGAGACCCTAGCTGGTGCGTCTTAAGTTGTCTTTGGTCATTGATGTCA
                                          ctttaat  putative branch site (score: 15)
                              tttgaaatat  TA-rich tract