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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCCGCGGATATTCGTGCGATGGACGCTTTGAGGCACGCCGACGCGAAAGTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattcggatctcacgttttctcctgattttcgcttgttttgacgccgcctacgtggtttcatttcttcacgtgatgttcatgtgtgagcagttga...

Basic information

species Physcomitrella patens
transcript PP1S47_158V6.1
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|22132799|gb|BQ827368.1|BQ827368
EST:     GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAG                         ATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
genomic: GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattc ... gctgtttcagATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
EST: gi|162257498|gb|FC433541.1|FC433541
EST:     GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAG                         ATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
genomic: GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattc ... gctgtttcagATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
EST: gi|162257499|gb|FC433542.1|FC433542
EST:     GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAG                         ATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
genomic: GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattc ... gctgtttcagATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
EST: gi|22492729|gb|BU052652.1|BU052652
EST:     GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAG                         ATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
genomic: GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattc ... gctgtttcagATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
EST: gi|162270344|gb|FC447044.1|FC447044
EST:     GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAG                         ATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
genomic: GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattc ... gctgtttcagATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
EST: gi|22133309|gb|BQ827664.1|BQ827664
EST:     GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAG                         ATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
genomic: GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattc ... gctgtttcagATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
EST: gi|22492565|gb|BU052488.1|BU052488
EST:     GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAG                         ATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC
genomic: GTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattc ... gctgtttcagATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCC

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), 35 (downstream exon)
Score: 261

GAGCCGCGGATATTCGTGCGATGGACGCTTTGAGGCACGCCGACGCGAAAGTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattc ... gctgtttcagATACAACCCCATGGCGAGGCTACGCTGGAAGAAGAACCGCGTGACCCACCCTGTTGGATACCAGAAGGCGAAGACGAGGGCGAGATTGAACTACATCAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCCGCGGATATTCGTGCGATGGACGCTTTGAGGCACGCCGACGCGAAAGTGCAGCATGCGACGCACCCAGCGGGAACAGCGCGGTGGAGAATGAACAGgtgcggattcggatctcacgttttctcctgattttcgcttgttttgacgccgcctacgtggtttcatttcttcacgtgatgttcatgtgtgagcagttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA