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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgtttatttctgtcggctgtcttgcattcacttccgggttctgacttagaatgtttgctcgcaaaccccttatttcggtttctgtcgcacgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT

Basic information

species Physcomitrella patens
transcript PP1S425_16V6.1
intron # 8
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|208385034|gb|DC919714.1|DC919714
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|162265881|gb|FC442884.1|FC442884
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|37829212|gb|BJ587224.1|BJ587224
EST:     TGAAGAGCCCGACAAGGAACCTTCCCCAAGGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: TGAAGAGCCCGACAAGGAACCTTCCCCAA-GGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|162186159|gb|FC361363.1|FC361363
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|37835343|gb|BJ593355.1|BJ593355
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|208364864|gb|DC943682.1|DC943682
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|208346039|gb|DC921284.1|DC921284
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|162173551|gb|FC350125.1|FC350125
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|162173550|gb|FC350124.1|FC350124
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|37850380|gb|BJ608388.1|BJ608388
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|208367233|gb|DC951221.1|DC951221
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
EST: gi|37832494|gb|BJ590506.1|BJ590506
EST:     ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAA                         GGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG
genomic: ATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCG

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: 31 (upstream exon), 29 (downstream exon)
Score: 17

GCGTGCCAATTTTAAGAAGCAAAATCCCGATGTTGAATCAGTAGGGGCTAATGAAGAGCCCGACAAGGAACCTTCCCCAAGGATGCGCTTTCGTCTAGAAgtaagtctat ... acgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttagaatgtttgctcgcaaaccccttatttcggtttctgtcgcacgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT
 ttctgac  putative branch site (score: 17)
                          ttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgtttatttctgtcggctgtcttgcattcacttccgggttctgacttagaatgtttgctcgcaaaccccttatttcggtttctgtcgcacgtgcacagGGATCGGAGCAAGAAATTGGAGAGGTTGCCCCTGATCATGACTTTGGAGCGTTGGAACTAGGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG