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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagcgttcggtcactgagatcaccgaagtagaaattagtgtctgtttacttgagaggatttccactcattcatgtatcctgcgatatttcgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATCGATCCTACGTACATGATCCGAGCCTGTCGAGCTAATGCTTCTGACCGAA

Basic information

species Physcomitrella patens
transcript PP1S94_106V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S94_106V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA01G03040.1 (Glycine max), 3'ss of exon 11
-taagcgttcggtcactgagatcaccgaagtagaaattagtgtctgtttacttgagaggatttccactcattcatgtatcctgcgatatttcgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATCGATCCTACGTACATGATCCGAGCCTGTCGAGCTAATGCTTCTGACCGAA
 |  | ||  |||  |||            || |      | ||||| | | |   |   |||  | ||| |  |  || |    |  |     | | |||   |||||  | || ||  | ||||| ||    || || || || || |||||||| |||||||||||||| || |||||||| |||||||||||  |||
ctttgagtatggtttctgttgcatattctata-atgcagatatctgtcttcatttaaattttttaaatcagtgtttcatgccaacaactgctttatttcagACGAAAAAATACTTCAAGGAAATTGGTGTTCATGCTGACGTTAAATATATCGATCCAACGTACATGATCCGTGCATGTCGAGCAAATGCTTCTGATGGAA
















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|67693514|gb|BJ953747.1|BJ953747
EST:     CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|162203811|gb|FC379908.1|FC379908
EST:     CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|162203812|gb|FC379909.1|FC379909
EST:     CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|37852524|gb|BJ610532.1|BJ610532
EST:     CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|7648346|gb|AW739329.1|AW739329
EST:     CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|18336359|gb|BJ168381.1|BJ168381
EST:     ACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: ACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|162229043|gb|FC404753.1|FC404753
EST:     CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|67697835|gb|BJ958068.1|BJ958068
EST:     TGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: TGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|162198099|gb|FC372126.1|FC372126
EST:     CTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACC-TACAAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACAT
genomic: CTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTAC-AAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACAT
EST: gi|37824275|gb|BJ582341.1|BJ582341
EST:     GGGAGACATAGGCGTTCNCCTTNCAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: GGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|37850516|gb|BJ608524.1|BJ608524
EST:     CCTCTGGAAACCCAGTCNTGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|7648257|gb|AW739240.1|AW739240
EST:     CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
EST: gi|100428968|gb|BY959524.1|BY959524
EST:     CTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGGAG                         -TAAAAAACCATTTT
genomic: CTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAG-AGgttagaactc ... cgcactgcagGTAAAAAACCATTTT
EST: gi|162229044|gb|FC404754.1|FC404754
EST:     CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG                         GTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC
genomic: CCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATC

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: 8 (upstream exon), 28 (downstream exon)
Score: 2

GATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAGgttagaactc ... cgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATCGATCCTACGTACATGATCCGAGCCTGTCGAGCTAATGCTTCTGACCGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacttgagaggatttccactcattcatgtatcctgcgatatttcgcactgcagGTAAAAAACCATTTTAAAAATATTGGAGTAGCAGCGGATGTGAAGTACATCGATCCTACGTACATGATCCGAGCCTGTCGAGCTAATGCTTCTGACCGAA
                                       atattt  TA-rich tract