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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGACGTGGCGAGACCATAAGGTGCACTATATAGTACAAGGCCAGGGTCCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttggtatgctcctgctcagagtcttttcaagattttaattctgtttcaagtttgtcttatttcagtttggagcgacagtctaagtgagctctacctgcag

Basic information

species Physcomitrella patens
transcript PP1S55_317V6.1
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|100407421|gb|BY991693.1|BY991693
EST:     CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAG                         GTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
genomic: CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
EST: gi|100452258|gb|CJ975180.1|CJ975180
EST:     CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAG                         GTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
genomic: CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
EST: gi|100446624|gb|CJ970923.1|CJ970923
EST:     CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAG                         GTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
genomic: CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
EST: gi|208364613|gb|DC935398.1|DC935398
EST:     CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCANCTTTCCATTGGAN                         GTATAACATCCCA
genomic: CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCA
EST: gi|100447341|gb|CJ971640.1|CJ971640
EST:     CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAG                         GTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
genomic: CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
EST: gi|100400504|gb|BY954510.1|BY954510
EST:     CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAG                         GTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
genomic: CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
EST: gi|100446257|gb|CJ970556.1|CJ970556
EST:     CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAG                         GTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
genomic: CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
EST: gi|67575917|gb|BJ948741.1|BJ948741
EST:     CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAG                         GTATAACATCCCAAAATTGGCTAAGACTCATACAGTCTACGCAATG
genomic: CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATG
EST: gi|162270100|gb|FC446800.1|FC446800
EST:     CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAG                         GTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT
genomic: CCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCT

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: 24 (upstream exon), 32 (downstream exon)
Score: 7

TTTGGACGTGGCGAGACCATAAGGTGCACTATATAGTACAAGGCCAGGGTCCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttgg ... ctacctgcagGTATAACATCCCAGAATTGGCTAAGACTCATACAGTCTACGCAATGGATCTCCTAGGATTTGGTTTCTCCGAGAAGGCATTGATAGATTACACCGCCGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGACGTGGCGAGACCATAAGGTGCACTATATAGTACAAGGCCAGGGTCCTCCTATTGTGCTGATTCACGGATTTGGTGCATCAGCTTTCCATTGGAGgtaggtttggtatgctcctgctcagagtcttttcaagattttaattctgtttcaagtttgtcttatttcagtttggagcgacagtctaagtgagctctacctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG