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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgactacttttttatccttttcttttctctccctcacccacaagcagcagtaattttcacgttcgaaactcacttaatttcttctaactggacttgaagGCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACCAGCAACGTTGGGGCTATCGTGGAAGAGAGCACTAAGCTCACTCATGATT

Basic information

species Physcomitrella patens
transcript PP1S53_92V6.2
intron # 10
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|162271773|gb|FC448906.1|FC448906
EST:     TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAG                         GCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC
genomic: TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAGgtgaatttct ... ggacttgaagGCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC
EST: gi|7648047|gb|AW739030.1|AW739030
EST:     TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAG                         GCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC
genomic: TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAGgtgaatttct ... ggacttgaagGCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC
EST: gi|162159654|gb|FC336040.1|FC336040
EST:     TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAG                         GCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC
genomic: TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAGgtgaatttct ... ggacttgaagGCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC
EST: gi|37827926|gb|BJ585938.1|BJ585938
EST:     TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAG                         GCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC
genomic: TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAGgtgaatttct ... ggacttgaagGCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC
EST: gi|162271772|gb|FC448905.1|FC448905
EST:     TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAG                         GCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC
genomic: TGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAGgtgaatttct ... ggacttgaagGCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACC

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: 3

AGAGAAGTATCTCGTCACATACAGTCTAAAGAAAAAGCGTGCATATGTTGTGATTAAGGAATCTGCTTCCTCTGATGATGTCGTTCGGGCTACCTTCCAGgtgaatttct ... ggacttgaagGCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACCAGCAACGTTGGGGCTATCGTGGAAGAGAGCACTAAGCTCACTCATGATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcagtaattttcacgttcgaaactcacttaatttcttctaactggacttgaagGCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACCAGCAACGTTGGGGCTATCGTGGAAGAGAGCACTAAGCTCACTCATGATT
                                     ttctaac  putative branch site (score: 3)
                             ttaatttcttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgactacttttttatccttttcttttctctccctcacccacaagcagcagtaattttcacgttcgaaactcacttaatttcttctaactggacttgaagGCACATGTAATGCTGCATATTTTACGAGGATTAAGAAGCACACTTATTACCAGCAACGTTGGGGCTATCGTGGAAGAGAGCACTAAGCTCACTCATGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - -cacaagc