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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTCGGGGTGTCGGTGAAGTCGACCGCTATGGGGCGCGAGGTTGACACCGAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaacgagttgcgcttcgtcttcgttgtctttgaggcagcaacgttttcttttcttgcttttgtgggtcggttgggcgtgttatcaatgggggcg...

Basic information

species Physcomitrella patens
transcript PP1S28_399V6.1
intron # 1
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|100367664|gb|BY984756.1|BY984756
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|100448697|gb|CJ972996.1|CJ972996
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|100399390|gb|BY954346.1|BY954346
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|162217577|gb|FC393981.1|FC393981
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208353466|gb|DC938701.1|DC938701
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208397465|gb|DC908299.1|DC908299
EST:     GAGGTGGAGGCCATGGATCCTCTGCANAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208367267|gb|DC939825.1|DC939825
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|100451948|gb|CJ975023.1|CJ975023
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208390214|gb|DC941993.1|DC941993
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208386359|gb|DC932855.1|DC932855
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208358240|gb|DC930681.1|DC930681
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|100434315|gb|BY979047.1|BY979047
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208377735|gb|DC940847.1|DC940847
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|18363121|gb|BJ195193.1|BJ195193
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|18329541|gb|BJ161547.1|BJ161547
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208374313|gb|DC940670.1|DC940670
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|100365672|gb|BY948358.1|BY948358
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|100368808|gb|BY984900.1|BY984900
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|100424955|gb|BY976899.1|BY976899
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208357909|gb|DC934828.1|DC934828
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208376707|gb|DC902916.1|DC902916
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|162215822|gb|FC390887.1|FC390887
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208345096|gb|DC909458.1|DC909458
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208375497|gb|DC937012.1|DC937012
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|208389975|gb|DC938030.1|DC938030
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|67703862|gb|BJ964095.1|BJ964095
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|162192625|gb|FC370672.1|FC370672
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|100388888|gb|BY988764.1|BY988764
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
EST: gi|100420599|gb|BY976088.1|BY976088
EST:     GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGA                         GTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA
genomic: GAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTA

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: 35 (upstream exon), 30 (downstream exon)
Score: 29

CGTTCGGGGTGTCGGTGAAGTCGACCGCTATGGGGCGCGAGGTTGACACCGAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaac ... ttctgtgcagGTGTATACTGGTGGATGAGAACGACAATGTTGTTGGCCATGACTCCAAGTACAACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTCGGGGTGTCGGTGAAGTCGACCGCTATGGGGCGCGAGGTTGACACCGAGGTGGAGGCCATGGATCCTCTGCAGAGGCGTCTCATGTTCGACGATGAgtgagtgaacgagttgcgcttcgtcttcgttgtctttgaggcagcaacgttttcttttcttgcttttgtgggtcggttgggcgtgttatcaatgggggcg

- - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG