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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacagactttgatcaatgaattttattttgtatcctcgtgacacttgagtcagagagatcgtgggtccagttattaaccgaggtctttttgtgtgtgcttgaaacttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAAGAATGTGGTATTCTCACAGAAGGTGGTCTTGTAGTCGAGGGACCTGATT

Basic information

species Physcomitrella patens
transcript PP1S8_288V6.1
intron # 24
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|162166640|gb|FC343532.1|FC343532
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|162180511|gb|FC356153.1|FC356153
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|162153113|gb|FC329519.1|FC329519
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|162155067|gb|FC330861.1|FC330861
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|162208804|gb|FC384940.1|FC384940
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|162191836|gb|FC367985.1|FC367985
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|162175273|gb|FC351471.1|FC351471
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|100413350|gb|BY956628.1|BY956628
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|100443051|gb|BY981677.1|BY981677
EST:     GACCAGACGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|162181321|gb|FC358416.1|FC358416
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
EST: gi|162205305|gb|FC380987.1|FC380987
EST:     GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAG                         GTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA
genomic: GACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAA

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: 35 (upstream exon), 34 (downstream exon)
Score: 69

GATCCTTGCAGACCAGGCGTGCGGGACGCTGTTGAAAGATGTCAAAAGGCTGGAGTGAAGgtgaacagac ... acttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAAGAATGTGGTATTCTCACAGAAGGTGGTCTTGTAGTCGAGGGACCTGATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtgggtccagttattaaccgaggtctttttgtgtgtgcttgaaacttgaacagGTTCGAATGGTTACAGGTGATAACAAGTTCACAGCCAAGGCAATTGCACAAGAATGTGGTATTCTCACAGAAGGTGGTCTTGTAGTCGAGGGACCTGATT
             tattaac  putative branch site (score: 69)
          agttattaa  TA-rich tract