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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctttgtttttcttgaaagagaaagagggcttgtattcgtcatgggagtcaaattattatgaagtaactagcttctgtcgtttttagtggactgatttcctcgtgctcgacttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACTGTTTCATAACCTCTTTCGCCGAAGCCAAGTTGCTTTAATGGCTTGTCGC

Basic information

species Physcomitrella patens
transcript PP1S131_16V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 16
gtttgtctttgtttttcttgaaagagaaagagggcttgtattcgtcatgggagtcaaattattatgaagtaactagcttctgtcgtttttagtggactgatttcctcgtgctcgacttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACTGTTTCATAACCTCTTT-CGCCGAAGCCAAGTTGCTTTAATGGCTTGTCGC
  || ||||| || || || |             ||| | ||   | |     |  ||||| |     || |||   | |||||  ||||      ||  | |  || |  |  | || | |||||||| ||||| || ||||| |||||||||||| || |||| ||||| |||||||  |||  | |         |     ||   |||  |||    |   
--ttttcttttttctttttaatttc---------cttctttttaacttt----tttaattactggttggtcact--ttgctgtctatttt------ctcttcttttctttttt-atttttacagGAAAAATGGTCCAAAAATCTCTACATTGCAGCAATTTGTTATGGGCGAACTGTTTGTTAATTTGTGGATTGTATATTTTTGTGATTTTGGTGGAGAATAT-
















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|162163673|gb|FC340285.1|FC340285
EST:     AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAG                         GAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
genomic: AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
EST: gi|162228109|gb|FC405691.1|FC405691
EST:     AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAG                         GAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
genomic: AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
EST: gi|162257791|gb|FC433989.1|FC433989
EST:     AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAG                         GAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
genomic: AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
EST: gi|162157366|gb|FC333169.1|FC333169
EST:     AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAG                         GAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
genomic: AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
EST: gi|37833992|gb|BJ592004.1|BJ592004
EST:     AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAG                         GAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
genomic: AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
EST: gi|162252530|gb|FC427339.1|FC427339
EST:     AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAG                         GAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
genomic: AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
EST: gi|100448451|gb|CJ972750.1|CJ972750
EST:     AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAG                         GAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
genomic: AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
EST: gi|37831666|gb|BJ589678.1|BJ589678
EST:     AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAG                         GAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
genomic: AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
EST: gi|162157367|gb|FC333170.1|FC333170
EST:     AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAG                         GAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT
genomic: AAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACT

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: 33 (upstream exon), 31 (downstream exon)
Score: 5

GGATCAGGCAGCCTTTGTTTTGAGTGTACCTCGGAGGAAGCCAGCTGATGAAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtcttt ... acttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACTGTTTCATAACCTCTTTCGCCGAAGCCAAGTTGCTTTAATGGCTTGTCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactagcttctgtcgtttttagtggactgatttcctcgtgctcgacttctgcagGAAAAGTGGTCTAAGAATCTTTACATTGCAGCAGTTAGTTACGGGCGGACTGTTTCATAACCTCTTTCGCCGAAGCCAAGTTGCTTTAATGGCTTGTCGC
                                              cttctgc  CT-rich tract
                tttttagt  TA-rich tract