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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattctattgtgagccgccatatttcccttctaatctcccgagtactgtgcaaccggcaatctgcaagttttatagtgggacttgtgcactcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAGACATGCAAGGTGTCCAGTTCATCAACACTGTACTCTCAGGATCGACCTT

Basic information

species Physcomitrella patens
transcript PP1S319_46V6.1
intron # 3
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|162239353|gb|FC416557.1|FC416557
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|208371438|gb|DC955774.1|DC955774
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|162220152|gb|FC396560.1|FC396560
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|162226254|gb|FC402962.1|FC402962
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|6227357|gb|AW155964.1|AW155964
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTTCCGTTTTCACGAATGGCAGTTGTCGACCAGGGGGTTGCATTTCGACA
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTT-CCGTTTTCACGAATG-CAGTTGTCGAC-AGGG--TTGCATT-CGACA
EST: gi|162248517|gb|FC425293.1|FC425293
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|162260313|gb|FC435616.1|FC435616
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|162260312|gb|FC435615.1|FC435615
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|7147910|gb|AW509832.1|AW509832
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGGTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACACATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|67691573|gb|BJ951806.1|BJ951806
EST:     GAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|162246699|gb|FC425292.1|FC425292
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|162226255|gb|FC402963.1|FC402963
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
EST: gi|208353885|gb|DC942783.1|DC942783
EST:     GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGG                         GTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG
genomic: GACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAG

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), 18 (downstream exon)
Score: 32

ACATTATCAGCCGCTCTCATGTCAGAAGCCAAATTCGATGGTGCTGACTTGACTGAAGTAATCATGTCGAAGGCATACGCAGTTGGAGCGAGCTTCAAGGgtaattcact ... tcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAGACATGCAAGGTGTCCAGTTCATCAACACTGTACTCTCAGGATCGACCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgcaaccggcaatctgcaagttttatagtgggacttgtgcactcttacgcagGTTCCGTTTTCACGAATGCAGTTGTCGACAGGGTTGCATTCGACAAATCAGACATGCAAGGTGTCCAGTTCATCAACACTGTACTCTCAGGATCGACCTT
                                            ctcttac  putative branch site (score: 32)
                                          cactctt  CT-rich tract
                    aagttttata  TA-rich tract