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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaccgtttttagagacaaaaggagtgagcactaacactatcatctgtttacttgatttaacacgtgatttcggggttattttttgtggttttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTAAACCTACTTGGTTTCTGTATTTTTGAAATGTGTGTGGGAGTGTTCTGGC

Basic information

species Physcomitrella patens
transcript PP1S8_271V6.1
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|162192969|gb|FC371952.1|FC371952
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|162272122|gb|FC447916.1|FC447916
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|37851200|gb|BJ609208.1|BJ609208
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|18334427|gb|BJ166444.1|BJ166444
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|208374375|gb|DC948407.1|DC948407
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|18334290|gb|BJ166307.1|BJ166307
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|18333333|gb|BJ165347.1|BJ165347
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|162160906|gb|FC336969.1|FC336969
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|208365737|gb|DC944165.1|DC944165
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|162160905|gb|FC336968.1|FC336968
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|162186224|gb|FC362156.1|FC362156
EST:     TCGTGTTNGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|37824740|gb|BJ582806.1|BJ582806
EST:     GCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: GCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|162272123|gb|FC447917.1|FC447917
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|37851199|gb|BJ609207.1|BJ609207
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|162187638|gb|FC364095.1|FC364095
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|162274079|gb|FC450151.1|FC450151
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|208356198|gb|DC946246.1|DC946246
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCTGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|37824742|gb|BJ582808.1|BJ582808
EST:     CGTCGCTTCGGGTTCCNTCTGCNTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCNTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: CGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
EST: gi|162192968|gb|FC371951.1|FC371951
EST:     TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAA                         TTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA
genomic: TCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTA

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: 19 (upstream exon), 30 (downstream exon)
Score: 4

ATCTCGTCTCATGTCACGTTCACACTTGAGGGTGGAGAGCTATATGCAGGTCGTGTTTGCCGTCGCTTCGGGTTCCCTCTGCCTTCCAGTTATCATCCAAgtgagttcat ... tttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTAAACCTACTTGGTTTCTGTATTTTTGAAATGTGTGTGGGAGTGTTCTGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttacttgatttaacacgtgatttcggggttattttttgtggttttgttgcagTTCTTTTTGCCAGACTCACCCTCTGATAGCATTACCGCTGGGGGGCGACTAAACCTACTTGGTTTCTGTATTTTTGAAATGTGTGTGGGAGTGTTCTGGC
          atttaac  putative branch site (score: 4)
                                            ttttgtt  putative PPT
                               ttattttttgt  TA-rich tract