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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaacttctctacattttgggtgtctctgatactttgctactctgacactctgcaacttatgaagtcttcctgtttgacaattgaagaaaaaac...

Basic information

species Physcomitrella patens
transcript PP1S37_33V6.2
intron # 9
splice site 5'
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|162194038|gb|FC370213.1|FC370213
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCCGCT-GC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCC-GCTTGC
EST: gi|162202113|gb|FC378034.1|FC378034
EST:     ACTGAAAGTGAATTCGCANAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
EST: gi|162165709|gb|FC340890.1|FC340890
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
EST: gi|67574071|gb|BJ946895.1|BJ946895
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCT
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCT
EST: gi|208373915|gb|DC940426.1|DC940426
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
EST: gi|208363044|gb|DC957985.1|DC957985
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
EST: gi|162176173|gb|FC351915.1|FC351915
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
EST: gi|162233299|gb|FC409849.1|FC409849
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
EST: gi|208362586|gb|DC939510.1|DC939510
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCA-                         GTACTGGGAACCAGTT
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTT
EST: gi|100352729|gb|BY945419.1|BY945419
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
EST: gi|19783472|gb|BQ040017.1|BQ040017
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
EST: gi|162258522|gb|FC434737.1|FC434737
EST:     ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAA                         GTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC
genomic: ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCC

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), 31 (downstream exon)
Score: 30

ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaa ... atttatacagGTACTGGGAACCAGTTTATGAGGACTCTATGAATCTGATTGCCCGCTTGCCAGAGTTAGCTGCGTACATATATCGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGAAAGTGAATTCGCAAAGGCTTACGAAGGCGGATTGCACAAGAGCAAgtatgttcaacttctctacattttgggtgtctctgatactttgctactctgacactctgcaacttatgaagtcttcctgtttgacaattgaagaaaaaac

- - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - -  AGAGCA