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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggttgcttgactgcggctattaggatggtatagttgttacgtgggctgttcagaagataattcagagttaattcttatgcttatgttgtgattctccagCTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGACGGACGGTCACTCTTGAGCCTGAGAAAGGTGCACAGGTATCGGGCTGTGCCTATCGAGTATC

Basic information

species Physcomitrella patens
transcript PP1S56_10V6.1
intron # 2
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|100445429|gb|CJ975578.1|CJ975578
EST:     TGAACGTGTTGTAGGGTTCATCANGGGCTATAGACGTGTGNTTAATCAAG                         CTAGCACTGATCACCGTGGGACTCC
genomic: TGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTAATCAAGgtaatttgag ... gattctccagCTAGCACTGATCACCGTGGGACTCC
EST: gi|208397844|gb|DC916165.1|DC916165
EST:     TGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTAATCCAG                         CTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGACGGACGGTCACTC
genomic: TGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTAATCAAGgtaatttgag ... gattctccagCTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGACGGACGGTCACTC
EST: gi|208357745|gb|DC902297.1|DC902297
EST:     TGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTAATCAAG                         CTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGACGGACGGTCACTC
genomic: TGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTAATCAAGgtaatttgag ... gattctccagCTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGACGGACGGTCACTC
EST: gi|100441687|gb|BY962778.1|BY962778
EST:     TGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTAATCAAG                         CTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGA
genomic: TGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTAATCAAGgtaatttgag ... gattctccagCTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGA
EST: gi|100391020|gb|BY953030.1|BY953030
EST:     TGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTA-TCAAG                         CTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGACGGACGGTCACTC
genomic: TGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTAATCAAGgtaatttgag ... gattctccagCTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGACGGACGGTCACTC

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: 26 (upstream exon), 21 (downstream exon)
Score: 3

TGGGTATTTGGTTATGGTTCTCTAATTTGGAAGGCGGGTTTTGAGTACGATGAACGTGTTGTAGGGTTCATCAAGGGCTATAGACGTGTGTTTAATCAAGgtaatttgag ... gattctccagCTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGACGGACGGTCACTCTTGAGCCTGAGAAAGGTGCACAGGTATCGGGCTGTGCCTATCGAGTATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgttcagaagataattcagagttaattcttatgcttatgttgtgattctccagCTAGCACTGATCACCGTGGGACTCCCGAGTACCCTGGACGGACGGTCACTCTTGAGCCTGAGAAAGGTGCACAGGTATCGGGCTGTGCCTATCGAGTATC
                     agttaat  putative branch site (score: 3)
                                               ttctcc  putative PPT
                       ttaattcttat  TA-rich tract