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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgttcgctccttaggtattatgtgatgctcccggcagcacgtacaataatttgccactagcaaatttcatctcgaaaatgtaatatctaaatgagtcatatgatggttgagtctgctgatggtagctttatgaagtattggtaacttgtgtgggaagtaattttgatctgtattcacatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG

Basic information

species Physcomitrella patens
transcript PP1S78_210V6.2
intron # 3
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|67695361|gb|BJ955594.1|BJ955594
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|162208442|gb|FC384197.1|FC384197
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|162199764|gb|FC375837.1|FC375837
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|18341071|gb|BJ173104.1|BJ173104
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|162167356|gb|FC343059.1|FC343059
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|162167355|gb|FC343058.1|FC343058
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|162249723|gb|FC428163.1|FC428163
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|208346478|gb|DC917431.1|DC917431
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|18333668|gb|BJ165683.1|BJ165683
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|162179662|gb|FC355720.1|FC355720
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|37850040|gb|BJ608048.1|BJ608048
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|162185883|gb|FC360983.1|FC360983
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
EST: gi|162185882|gb|FC360982.1|FC360982
EST:     TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAAC                         GTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG
genomic: TTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTG

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: 21

TGATGGAGCCGTGACAGGAGTCAACGTGAAATTGGAAGAGAATAAGCTTATTGTTCAGAAGTGGAGATTTAACAGTTGGGCTGATGGTCACTATTCGAACgtaagtcgtt ... acatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagtattggtaacttgtgtgggaagtaattttgatctgtattcacatgttcagGTGATCCTGTCTTTTGAGGAGCCGGAAGTTGGCTTGACTGTGGTGAAACTGACTCAGACGAACGTTCCAGACGAGGACAG
                        aagtaatttt  TA-rich tract