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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttttttgttattatgtgaactttgcatgagttgggttaggatacagttgacctatacgtttgataacgcgttttgctgctacaaatatgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTGAGGAATCCGCATTCGTGGCCCCCGGTGCTTCTGTTGTTGGTGAAGTGGA

Basic information

species Physcomitrella patens
transcript PP1S207_12V6.1
intron # 1
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|18369330|gb|BJ201416.1|BJ201416
EST:     AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGG                         TTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
genomic: AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
EST: gi|18363020|gb|BJ195092.1|BJ195092
EST:     AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGG                         TTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
genomic: AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
EST: gi|208349491|gb|DC905629.1|DC905629
EST:     AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGG                         TTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
genomic: AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
EST: gi|67697542|gb|BJ957775.1|BJ957775
EST:     CAAAGATGAGG                         TTTCCAAGCATCAAACCG-TTTAAGCATATTTGACAAGAAGCCTGTCATTG
genomic: CAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
EST: gi|18353257|gb|BJ185312.1|BJ185312
EST:     AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGG                         TTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
genomic: AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
EST: gi|18350228|gb|BJ182279.1|BJ182279
EST:     AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGG                         TTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
genomic: AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
EST: gi|208381510|gb|DC919512.1|DC919512
EST:     CGTCTCNGTTCACGC-TGCAAGGCGGCAACACGNTCAAAGATGAGG                         TTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
genomic: CGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
EST: gi|37850643|gb|BJ608651.1|BJ608651
EST:     TCAAAGATGAGG                         TTTCCAAGCATCAANCCGTTTTAAGCATATTNGACAAGAAGCCTGTCATTG
genomic: TCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
EST: gi|67574145|gb|BJ946969.1|BJ946969
EST:     AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGG                         TTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
genomic: AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
EST: gi|162233652|gb|FC409411.1|FC409411
EST:     AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGG                         TTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG
genomic: AGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTG

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: 27 (upstream exon), 34 (downstream exon)
Score: 7

CGAGTGGTCTTCTCTCTGGGCAAGGCTGCGCGCACCACCGGCCAAGCTCTAGATCGTCTCGGTTCACGCTTGCAAGGCGGCAACACGTTCAAAGATGAGGgtaagagatt ... tgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTGAGGAATCCGCATTCGTGGCCCCCGGTGCTTCTGTTGTTGGTGAAGTGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagttgacctatacgtttgataacgcgttttgctgctacaaatatgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTGAGGAATCCGCATTCGTGGCCCCCGGTGCTTCTGTTGTTGGTGAAGTGGA
                  tgataac  putative branch site (score: 7)
                                     tacaaatat  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttttttgttattatgtgaactttgcatgagttgggttaggatacagttgacctatacgtttgataacgcgttttgctgctacaaatatgatctgcagTTTCCAAGCATCAAACCGTTTTAAGCATATTTGACAAGAAGCCTGTCATTGAGGAATCCGCATTCGTGGCCCCCGGTGCTTCTGTTGTTGGTGAAGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA