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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcctcaatgtatcacacaactgattgcattgttggacttcttttggaccatctttttcaggacactttaaagaagagttatcgagtgtattatt...

Basic information

species Physcomitrella patens
transcript PP1S58_148V6.4
intron # 5
splice site 5'
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|67718017|gb|BJ968276.1|BJ968276
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|162200956|gb|FC377359.1|FC377359
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|208368341|gb|DC935682.1|DC935682
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|100371545|gb|BY968032.1|BY968032
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|67718144|gb|BJ968403.1|BJ968403
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|67718550|gb|BJ968809.1|BJ968809
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|100369047|gb|BY984997.1|BY984997
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|100439827|gb|BY980259.1|BY980259
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTTCA-CTTACGGACAGGCTGCCCTCTA-TCTCGTTGCTGGG
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTT-CAACTTACGGACAGGCTGCC-TCTAATCTCGTTGCTGGG
EST: gi|18342937|gb|BJ174973.1|BJ174973
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|67716636|gb|BJ966896.1|BJ966896
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGA-
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|67718192|gb|BJ968451.1|BJ968451
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|67702885|gb|BJ963118.1|BJ963118
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTT
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTT
EST: gi|162158680|gb|FC335047.1|FC335047
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|162261438|gb|FC438274.1|FC438274
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|67717915|gb|BJ968174.1|BJ968174
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|100440952|gb|BY962440.1|BY962440
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|162150756|gb|FC327028.1|FC327028
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|208390566|gb|DC937498.1|DC937498
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
EST: gi|208389212|gb|DC933240.1|DC933240
EST:     TACGTCTGCACCAGCAACTACCACTGGCCTATC                         AGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA
genomic: TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAA

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), 35 (downstream exon)
Score: 16

TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcct ... attgatgcagAGCTCCCGCTTCAACTTACGGACAGGCTGCCTCTAATCTCGTTGCTGGGAATGTTCTGGAGACCACCGTACAACAGATTATGGATATGGGTGGGGGTAGC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACGTCTGCACCAGCAACTACCACTGGCCTATCgtatgttcctcaatgtatcacacaactgattgcattgttggacttcttttggaccatctttttcaggacactttaaagaagagttatcgagtgtattatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaga