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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttggttttaccctcgtttattcttgcatttttttcgtttcttgtgtttatgattgtgtgttttacgtgaattttgttatgaagttcagtctaca...

Basic information

species Physcomitrella patens
transcript PP1S25_89V6.2
intron # 6
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|67697971|gb|BJ958204.1|BJ958204
EST:     ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG                         ATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
genomic: ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttgg ... tggtttgcagATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
EST: gi|162273472|gb|FC449617.1|FC449617
EST:     ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG                         ATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
genomic: ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttgg ... tggtttgcagATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
EST: gi|208354191|gb|DC957411.1|DC957411
EST:     ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG                         ATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
genomic: ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttgg ... tggtttgcagATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
EST: gi|208361426|gb|DC935113.1|DC935113
EST:     ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCANGCGCAG                         ATGATGAATCCTGGCANCTACCAGGTTCA-CATTAT-AGTAT-ACAGGCTT
genomic: ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttgg ... tggtttgcagATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
EST: gi|162273471|gb|FC449616.1|FC449616
EST:     ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG                         ATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
genomic: ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttgg ... tggtttgcagATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
EST: gi|37828975|gb|BJ586987.1|BJ586987
EST:     ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG                         ATGATGAATCCTGGCAACTA-CAGGTTCAACATTATTAGTATTACAGGCTT
genomic: ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttgg ... tggtttgcagATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
EST: gi|208387454|gb|DC949239.1|DC949239
EST:     ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAG                         ATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT
genomic: ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttgg ... tggtttgcagATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTT

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: 7

ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttgg ... tggtttgcagATGATGAATCCTGGCAACTACCAGGTTCAACATTATTAGTATTACAGGCTTCTGTTTCTGCATCTTTGAAATGACAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTGCAGCAAGGAGGCTATAACCCTTACATGCAAGCGCAGgtttgtttggttttaccctcgtttattcttgcatttttttcgtttcttgtgtttatgattgtgtgttttacgtgaattttgttatgaagttcagtctaca

- - -  AGCAAG
- - - - - AAGGAG