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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGGTATGAAACCCTAGAGCCAGCTTCGAAGCTTTCTCTCTTCGTCGCAATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagtatcctttttctcaattcctgcttcgttgtgtaatgtctccttcttcgctttgttattagattctgtgtctcctttgaaacccactcttgtc...

Basic information

species Physcomitrella patens
transcript PP1S22_76V6.1
intron # 1
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|67694098|gb|BJ954331.1|BJ954331
EST:     ATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: ATACGTCTCTCCCTGGCTGGGCGCTGTT-CCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162270731|gb|FC446344.1|FC446344
EST:     ATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCNGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: ATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACC-GTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162227758|gb|FC402686.1|FC402686
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|18350710|gb|BJ182761.1|BJ182761
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162262298|gb|FC437625.1|FC437625
EST:     TCTCTCCCTGGCTGGGCGCTGTTCCCCCACCNGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: TCTCTCCCTGGCTGGGCGCTGTTCCCCCACC-GTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|19781574|gb|BQ039741.1|BQ039741
EST:     CTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: CTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162273803|gb|FC449734.1|FC449734
EST:     GTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: GTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|18365111|gb|BJ197185.1|BJ197185
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|18363914|gb|BJ195986.1|BJ195986
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|18361968|gb|BJ194035.1|BJ194035
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162224837|gb|FC400837.1|FC400837
EST:     CCCCNCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: CCCC-CACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|18364653|gb|BJ196726.1|BJ196726
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|67692927|gb|BJ953160.1|BJ953160
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162270730|gb|FC446343.1|FC446343
EST:     TGGCTGGGCGCTGTTCCCCCACCGTTNTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: TGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162272796|gb|FC447978.1|FC447978
EST:     CCCCCACCNGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: CCCCCACC-GTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|67570800|gb|BJ943624.1|BJ943624
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162205890|gb|FC381336.1|FC381336
EST:     CGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCNGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: CGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACC-GTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|18365599|gb|BJ197676.1|BJ197676
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|18345004|gb|BJ177045.1|BJ177045
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|18352797|gb|BJ184852.1|BJ184852
EST:     AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: AATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|67569660|gb|BJ942484.1|BJ942484
EST:     ATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: ATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCG-TTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162273804|gb|FC449735.1|FC449735
EST:     GGCGCTGTTCCCCCACCNGTTTTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: GGCGCTGTTCCCCCACC-GTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
EST: gi|162227744|gb|FC402685.1|FC402685
EST:     GGGCGCTGTTCCCCCACCGTTNTTCGACATG                         GTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG
genomic: GGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG

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: 34 (upstream exon), 34 (downstream exon)
Score: 16

GGCGGGTATGAAACCCTAGAGCCAGCTTCGAAGCTTTCTCTCTTCGTCGCAATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagta ... tgattcacagGTCAAGTACGCGAGGGACCCGGTGAATGCCACCAAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGGGTATGAAACCCTAGAGCCAGCTTCGAAGCTTTCTCTCTTCGTCGCAATACGTCTCTCCCTGGCTGGGCGCTGTTCCCCCACCGTTTTTCGACATGgtacgcagtatcctttttctcaattcctgcttcgttgtgtaatgtctccttcttcgctttgttattagattctgtgtctcctttgaaacccactcttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT