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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggttgcttcattgatatggcagtgaagtgcgtgtttatcttatttaagtgattctattttattttattttgttttattttaaagttcaaactactttttcaaactttattttaaatgatgcttttcaagaggtttgctttgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG

Basic information

species Physcomitrella patens
transcript PP1S76_197V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgaggttgcttcattgatatggcagtgaagtgcgtgtttatcttatttaagtgattctattttattttattttgttttattttaaagttcaaactactttttcaaactttattttaaatga-tgcttttcaagaggtttgctttgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG
                                                                            |  |  | | |   |    |  || |  |   | | |   |  | | |  | ||        |   | | |||| |||||  |  |||||||||| |||||||||||||| || || || || ||| | |||||||||||||||||||| || 
---------------------------------------------------------------------------gtgaaagtcataagacggcttggttctctattttctttgccagttaaatattgttttgttaactccatgttaatttcagGCTATCCGGCGACGTTTTGACAAGCGTATCTATATTCCTCTCCCAGAGGCCAAGGCTCGGCAGCACATGTTCAAA
















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|162261190|gb|FC437207.1|FC437207
EST:     TTAGCTGCTACAAATACGCCCTACTCTTTGGATCAG                         GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
genomic: TTAGCTGCTACAAATACGCCCTACTCTTTGGATCAGgtgaggttgc ... tgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
EST: gi|162243142|gb|FC416742.1|FC416742
EST:     CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAG                         GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
genomic: CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAGgtgaggttgc ... tgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
EST: gi|162268434|gb|FC444203.1|FC444203
EST:     CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAG                         GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
genomic: CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAGgtgaggttgc ... tgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
EST: gi|162189691|gb|FC366329.1|FC366329
EST:     CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAG                         GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
genomic: CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAGgtgaggttgc ... tgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
EST: gi|162196818|gb|FC373886.1|FC373886
EST:     CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAG                         GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
genomic: CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAGgtgaggttgc ... tgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
EST: gi|162149983|gb|FC326514.1|FC326514
EST:     GGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAG                         GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
genomic: GGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAGgtgaggttgc ... tgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
EST: gi|208397729|gb|DC911980.1|DC911980
EST:     CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAG                         GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGANTCT
genomic: CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAGgtgaggttgc ... tgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
EST: gi|162196819|gb|FC373887.1|FC373887
EST:     CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAG                         GCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT
genomic: CTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAGgtgaggttgc ... tgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCT

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: 34 (upstream exon), 33 (downstream exon)
Score: 14

GGTGTCGGCAATCAAGACACTAAGGTTCTTGTGTTAGCTGCTACAAATACGCCCTACTCTTTGGATCAGgtgaggttgc ... tgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcaaactttattttaaatgatgcttttcaagaggtttgctttgaattgcagGCGGTGAGGCGACGTTTCGACAAGCGTATCTACATCCCACTACCGGAGTCTAAGGCTCGGCAGCACATGTTTAAG
                                      tttgcttt  CT-rich tract
          tttattttaaatgatg  TA-rich tract