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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaagtatcaaattgattctttatcatgcaaattagctccacttattatttacagaatctctctctggttggtcttcaaaaattccataggcttgcattcgacctctcttgacaccattgttttgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGAGACTGGAAAGGTTGTTGAGTTCATCAAGTTCGATATTGGCAACATTGTT

Basic information

species Physcomitrella patens
transcript PP1S2_16V6.1
intron # 5
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|67716905|gb|BJ967164.1|BJ967164
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208391390|gb|DC933567.1|DC933567
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208389935|gb|DC937766.1|DC937766
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208392913|gb|DC928599.1|DC928599
EST:     TTCGATGGCCGGACCNNTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: TTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208376484|gb|DC922515.1|DC922515
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|162236728|gb|FC413407.1|FC413407
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|67719943|gb|BJ970202.1|BJ970202
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|18361523|gb|BJ193589.1|BJ193589
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|162192347|gb|FC371642.1|FC371642
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208382233|gb|DC914852.1|DC914852
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|162279719|gb|FC455627.1|FC455627
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|67728248|gb|BJ978507.1|BJ978507
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATCGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAGGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|162279720|gb|FC455628.1|FC455628
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208368148|gb|DC947708.1|DC947708
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|18365612|gb|BJ197689.1|BJ197689
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208378974|gb|DC922820.1|DC922820
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|162194794|gb|FC371641.1|FC371641
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|67695781|gb|BJ956014.1|BJ956014
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACNGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|67573065|gb|BJ945889.1|BJ945889
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208382671|gb|DC923257.1|DC923257
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|162236729|gb|FC413408.1|FC413408
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|162190584|gb|FC366222.1|FC366222
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|67572408|gb|BJ945232.1|BJ945232
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|67728201|gb|BJ978460.1|BJ978460
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|67719989|gb|BJ970248.1|BJ970248
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATCGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAGGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|67696449|gb|BJ956682.1|BJ956682
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208400408|gb|DC908635.1|DC908635
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208390785|gb|DC945858.1|DC945858
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
EST: gi|208362881|gb|DC950831.1|DC950831
EST:     GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAG                         GTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA
genomic: GGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGA

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), 35 (downstream exon)
Score: 11

TACAAGCTGTGCAAGGTCAGGTCTGCTCAGTTTGGAGACAAGGGCGTACCACACATTACCACTTTCGATGGCCGGACCATTAGgtatggaagt ... tgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGAGACTGGAAAGGTTGTTGAGTTCATCAAGTTCGATATTGGCAACATTGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattccataggcttgcattcgacctctcttgacaccattgttttgcatgtaagGTACCCGGACCCCCTTATCAAGGCCAACGATACTGTCAAGATCAATCTTGAGACTGGAAAGGTTGTTGAGTTCATCAAGTTCGATATTGGCAACATTGTT
                            tcttgac  putative branch site (score: 11)
                                       ttgtttt  putative PPT
                                      attgtttt  TA-rich tract