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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgtcttcgtcctcctctatacgctcctgtttcccaacccgttttacacagtttttaacactacgctgtactccgaagctcctacaaaagctctgacaaagcggcgattagttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG

Basic information

species Physcomitrella patens
transcript PP1S336_61V6.1
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|67691914|gb|BJ952147.1|BJ952147
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|162259361|gb|FC436226.1|FC436226
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|37841635|gb|BJ599643.1|BJ599643
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|37844729|gb|BJ602737.1|BJ602737
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|37841219|gb|BJ599227.1|BJ599227
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|162259347|gb|FC436225.1|FC436225
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|18338709|gb|BJ170733.1|BJ170733
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|37839303|gb|BJ597311.1|BJ597311
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|67699873|gb|BJ960106.1|BJ960106
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|37852673|gb|BJ610681.1|BJ610681
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|37846475|gb|BJ604483.1|BJ604483
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|37850166|gb|BJ608174.1|BJ608174
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|37843528|gb|BJ601536.1|BJ601536
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
EST: gi|18339385|gb|BJ171412.1|BJ171412
EST:     ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTG                         GTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA
genomic: ACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGA

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: 31 (upstream exon), 29 (downstream exon)
Score: 3

AGGAGCCTGTGTGGGTCATGAATGCCATGCCTCCGGAAGCTAAAGTTGACACTCTGGGCGTGATCTTCGAGCGTGGTTTTATTGGAACTTATCAGAACTGgtaacgtctt ... ttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtactccgaagctcctacaaaagctctgacaaagcggcgattagttgtgatcagGTGCGAGGCATTCTCCACGTATCCACGAACCTACGACCTGATCCACGCAGACAAAGTTTTCAGCATGTACCAAGACAG
                        ctctgac  putative branch site (score: 3)
                tacaaaa  TA-rich tract