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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAATTGATGCAAATTGATTTGCAGTCTCATGAGCGTTGGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgctgacctttctgacttaaacctctaaagtacgagctcactacaaaagtcaagaggaggttttggaccacattttaataatttcatgacaat...

Basic information

species Physcomitrella patens
transcript PP1S93_48V6.1
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|162250870|gb|FC426914.1|FC426914
EST:     GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAG                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|162157103|gb|FC333673.1|FC333673
EST:     GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAG                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|37844012|gb|BJ602020.1|BJ602020
EST:     CCGTACGTTTTATTGGGAGCCGGAGCAAGTGAG                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: CCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|162158928|gb|FC334801.1|FC334801
EST:     GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAN                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|19781537|gb|BQ039733.1|BQ039733
EST:     GGAGCCGGAGCAAGTGAG                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: GGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|162191113|gb|FC367375.1|FC367375
EST:     GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAG                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|162193300|gb|FC370918.1|FC370918
EST:     GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAG                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|162166947|gb|FC343332.1|FC343332
EST:     GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAG                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|162152767|gb|FC329773.1|FC329773
EST:     GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAG                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|100430081|gb|BY978237.1|BY978237
EST:     GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAG                         GTCGAGGTTAACCTGTTAACAGGGGAAACAAGGATCTTGGCTGTGGATCTT
genomic: GGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
EST: gi|37838554|gb|BJ596562.1|BJ596562
EST:     CCGTACGTTTTATTTGGAGCCGGAGCAAGTGAG                         NTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT
genomic: CCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTT

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: 33 (upstream exon), 32 (downstream exon)
Score: 12

GCCAAATTGATGCAAATTGATTTGCAGTCTCATGAGCGTTGGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgc ... acatttgcagGTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAAATTGATGCAAATTGATTTGCAGTCTCATGAGCGTTGGGTTTCTCCCATGAAACCGTACGTTTTATTTGGAGCCGGAGCAAGTGAGgtgtgattgctgacctttctgacttaaacctctaaagtacgagctcactacaaaagtcaagaggaggttttggaccacattttaataatttcatgacaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG