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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACCTGAAGATACCTCAGTATCGAAGGTCATGACGAAGAATCCTGTCTTTGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtactattcattacttttgttttgtaaaaggttaaaaccttagcgtgtataattcagatagtctgatctgaaatttcagctagattggtagacat...

Basic information

species Physcomitrella patens
transcript PP1S86_24V6.1
intron # 3
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|100392285|gb|BY953287.1|BY953287
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAG                         GCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
EST: gi|18330771|gb|BJ162777.1|BJ162777
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAG                         GCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
EST: gi|18342907|gb|BJ174943.1|BJ174943
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAG                         GCAAGTTCAGGCATTTGCCTGTAGTGGA
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGA
EST: gi|100383782|gb|BY969311.1|BY969311
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAG                         GCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
EST: gi|18346829|gb|BJ178874.1|BJ178874
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAG                         GCAAGTTCAGGCATTTGCCTGTAG
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAG
EST: gi|100446857|gb|CJ971156.1|CJ971156
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAG                         GCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
EST: gi|18331556|gb|BJ163567.1|BJ163567
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAG                         GCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGG
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGG
EST: gi|162166444|gb|FC342426.1|FC342426
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAG                         GCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC
EST: gi|18330917|gb|BJ162923.1|BJ162923
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAG                         GCAAGTTCAGGCATTTGCCTGTAGTGGAGAA
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAA
EST: gi|100352242|gb|BY983110.1|BY983110
EST:     TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCCAG                         GCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAAAGGTTGTTGCACTTC
genomic: TGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTC

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), 35 (downstream exon)
Score: 14

AGACCTGAAGATACCTCAGTATCGAAGGTCATGACGAAGAATCCTGTCTTTGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtact ... tttgtgacagGCAAGTTCAGGCATTTGCCTGTAGTGGAGAATGGAGAGGTTGTTGCACTTCTGGATATCACAAAATGTCTCTACGATGCTATTGCTCGCATGGAGCGGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACCTGAAGATACCTCAGTATCGAAGGTCATGACGAAGAATCCTGTCTTTGTTATGGGAGATACTCTTGCAGTGGAAGCATTACAGAAGATGGTTCAAGgtgctgtactattcattacttttgttttgtaaaaggttaaaaccttagcgtgtataattcagatagtctgatctgaaatttcagctagattggtagacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG