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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagtgatcgtctcatagctgggccatattttttgtgtcgtaggttgacgtgtttcctgtacattccaggcgtgtaacgacaagctttgtggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACATCCATCAATACTCTCGGAGACGAAGTTCACTCCAGCTCATCTGATCTGGT

Basic information

species Physcomitrella patens
transcript PP1S15_388V6.3
intron # 1
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|100408717|gb|BY974252.1|BY974252
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|100397537|gb|BY990276.1|BY990276
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|100398934|gb|BY990589.1|BY990589
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|18373365|gb|BJ204943.1|BJ204943
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|18361160|gb|BJ193225.1|BJ193225
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|100436924|gb|BY979594.1|BY979594
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|208391692|gb|DC942282.1|DC942282
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|100390523|gb|BY952931.1|BY952931
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|18358749|gb|BJ190808.1|BJ190808
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|18331585|gb|BJ163596.1|BJ163596
EST:     TTTAGTAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|162262231|gb|FC437142.1|FC437142
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|67576309|gb|BJ949133.1|BJ949133
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
EST: gi|100390179|gb|BY952587.1|BY952587
EST:     TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGG                         GTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT
genomic: TTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACAT

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), 25 (downstream exon)
Score: 7

TGACGCAGTGGAGGACGTTTGTTCGGTTTCGGTGCAAGTAGATCTTACTATTTAGGAGTGATCCGACTTGAAGCGAGGGCGAGTGGTTCTTTCGCCGAGGgtaagtaagt ... ggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACATCCATCAATACTCTCGGAGACGAAGTTCACTCCAGCTCATCTGATCTGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacgtgtttcctgtacattccaggcgtgtaacgacaagctttgtggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACATCCATCAATACTCTCGGAGACGAAGTTCACTCCAGCTCATCTGATCTGGT
                          gtgtaac  putative branch site (score: 7)
                                               ttaatta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagtgatcgtctcatagctgggccatattttttgtgtcgtaggttgacgtgtttcctgtacattccaggcgtgtaacgacaagctttgtggttaattagGTATTGATTTTGTGGGCGGGATTTGTACGCAACACTGCACTGTATCAACATCCATCAATACTCTCGGAGACGAAGTTCACTCCAGCTCATCTGATCTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA