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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcactttctcaatgcatcacggcttttgggacagattcttgtcttcttgatttgttaaatgctgaatttgtcaagcctcgatggttacgtatcttgttatcgtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGGAGGCAGCGCAAGCTATTAAACATATGGAGTTGGCCAAGGCCAAAAGGTA

Basic information

species Physcomitrella patens
transcript PP1S97_74V6.1
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|37850662|gb|BJ608670.1|BJ608670
EST:     TTCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: TTCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|37829134|gb|BJ587146.1|BJ587146
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162274404|gb|FC450431.1|FC450431
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162274878|gb|FC451113.1|FC451113
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162262677|gb|FC438472.1|FC438472
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162235235|gb|FC412111.1|FC412111
EST:     AGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: AGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18369346|gb|BJ201432.1|BJ201432
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|37844465|gb|BJ602473.1|BJ602473
EST:     TTCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGG
genomic: TTCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCC-AGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGG
EST: gi|162274403|gb|FC450430.1|FC450430
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|37823916|gb|BJ581982.1|BJ581982
EST:     CGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: CGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162266465|gb|FC442501.1|FC442501
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18346854|gb|BJ178899.1|BJ178899
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|37822217|gb|BJ580283.1|BJ580283
EST:     TCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: TCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18360908|gb|BJ192972.1|BJ192972
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18353902|gb|BJ185957.1|BJ185957
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|37827543|gb|BJ585555.1|BJ585555
EST:     TTCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: TTCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162272845|gb|FC448820.1|FC448820
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18348254|gb|BJ180301.1|BJ180301
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|37852997|gb|BJ611005.1|BJ611005
EST:     GCAATGGTGAAGTACGCGAGAGATCCGGATAATGCNACGAAGG                         CCTGCAAGNCCAGAGGGTCGGATTNGCGAGTNCATTTCAAGANCNCCAGGG
genomic: GCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|37838798|gb|BJ596806.1|BJ596806
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18343066|gb|BJ175104.1|BJ175104
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162203338|gb|FC378785.1|FC378785
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18373967|gb|BJ205545.1|BJ205545
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162266464|gb|FC442500.1|FC442500
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18367163|gb|BJ199244.1|BJ199244
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162272844|gb|FC448819.1|FC448819
EST:     TTTCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: TTTCGCAATGGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18350164|gb|BJ182215.1|BJ182215
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162235236|gb|FC412112.1|FC412112
EST:     GCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162230491|gb|FC407406.1|FC407406
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162201674|gb|FC377478.1|FC377478
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18344711|gb|BJ176752.1|BJ176752
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|18375101|gb|BJ206679.1|BJ206679
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
EST: gi|162262676|gb|FC438471.1|FC438471
EST:     GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG                         CCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG
genomic: GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGG

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), 34 (downstream exon)
Score: 42

GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGGgtatggcact ... gtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGGAGGCAGCGCAAGCTATTAAACATATGGAGTTGGCCAAGGCCAAAAGGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgctgaatttgtcaagcctcgatggttacgtatcttgttatcgtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGGAGGCAGCGCAAGCTATTAAACATATGGAGTTGGCCAAGGCCAAAAGGTA
      tgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcactttctcaatgcatcacggcttttgggacagattcttgtcttcttgatttgttaaatgctgaatttgtcaagcctcgatggttacgtatcttgttatcgtgaatgcagCCTGCAAGGCCAGAGGGTCGGATTTGCGAGTGCATTTCAAGAACACCAGGGAGGCAGCGCAAGCTATTAAACATATGGAGTTGGCCAAGGCCAAAAGGTA

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