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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctgcgcgggatccattcgcatcggtcgtgccacctattcattggagattgtaaaccatgcatgacaatctgagtgaggttgtaacttctctgtggcagGGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATGGGTTCATTGAAGGGCTTGAAGCTGTCAGCTGCCCCCGTTCGCCG

Basic information

species Physcomitrella patens
transcript PP1S309_73V6.2
intron # 2
splice site 3'
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|162180712|gb|FC357797.1|FC357797
EST:     TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGG                         GGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
genomic: TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGGgtaagcctcc ... tctgtggcagGGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
EST: gi|208362133|gb|DC943532.1|DC943532
EST:     TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGG                         GGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
genomic: TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGGgtaagcctcc ... tctgtggcagGGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
EST: gi|162156177|gb|FC332552.1|FC332552
EST:     TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGG                         GGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
genomic: TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGGgtaagcctcc ... tctgtggcagGGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
EST: gi|162268832|gb|FC445680.1|FC445680
EST:     TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGG                         GGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
genomic: TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGGgtaagcctcc ... tctgtggcagGGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
EST: gi|18330269|gb|BJ162275.1|BJ162275
EST:     TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGG                         GGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
genomic: TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGGgtaagcctcc ... tctgtggcagGGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
EST: gi|67701881|gb|BJ962114.1|BJ962114
EST:     TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGG                         GGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG
genomic: TGCAGGCTTCCTCTTCTACCAGAGGAGACGCCTCCATATCCTCCTCAGGGgtaagcctcc ... tctgtggcagGGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagattgtaaaccatgcatgacaatctgagtgaggttgtaacttctctgtggcagGGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATGGGTTCATTGAAGGGCTTGAAGCTGTCAGCTGCCCCCGTTCGCCG
                                   ttgtaac  putative branch site (score: 2)
                                         cttctctgt  CT-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgcgcgggatccattcgcatcggtcgtgccacctattcattggagattgtaaaccatgcatgacaatctgagtgaggttgtaacttctctgtggcagGGGTTTGCTCAGAAGAGCAATGTCACTTATTCCGCAGATGGATCTTTCATGGGTTCATTGAAGGGCTTGAAGCTGTCAGCTGCCCCCGTTCGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC