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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGCGGGACTAGAAGTAATCAAACGGTGTTGCACTTGCGATTGAAAGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttccttggctccatatttattatttttcgtgttatttttggcgttaacagcttgtgtggctgaagggagaaaaagctacgatgtgtgttggttttg...

Basic information

species Physcomitrella patens
transcript PP1S98_214V6.3
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|208387788|gb|DC941357.1|DC941357
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|208373484|gb|DC931901.1|DC931901
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|100388120|gb|BY988593.1|BY988593
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162239278|gb|FC416521.1|FC416521
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTG                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|208357378|gb|DC910719.1|DC910719
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|100433811|gb|BY960718.1|BY960718
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|18368067|gb|BJ200152.1|BJ200152
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|208352976|gb|DC910111.1|DC910111
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|100396293|gb|BY990058.1|BY990058
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162207218|gb|FC382540.1|FC382540
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|18361536|gb|BJ193602.1|BJ193602
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|18355092|gb|BJ187151.1|BJ187151
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162263590|gb|FC440100.1|FC440100
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162216213|gb|FC392630.1|FC392630
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162245832|gb|FC420473.1|FC420473
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|100431344|gb|BY960149.1|BY960149
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162252229|gb|FC425907.1|FC425907
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTG                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|162180414|gb|FC355835.1|FC355835
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|208354034|gb|DC930146.1|DC930146
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|22492564|gb|BU052487.1|BU052487
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|100449504|gb|CJ973792.1|CJ973792
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|208387483|gb|DC933346.1|DC933346
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCA---G                         GGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|208389484|gb|DC929423.1|DC929423
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCANGTG                         GGAANCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|100368940|gb|BY984950.1|BY984950
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|100384846|gb|BY969581.1|BY969581
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTG                         GGAAGCACGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|18363670|gb|BJ195742.1|BJ195742
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|100425661|gb|BY958707.1|BY958707
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|100384841|gb|BY969576.1|BY969576
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|18363004|gb|BJ195076.1|BJ195076
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
EST: gi|18375323|gb|BJ206901.1|BJ206901
EST:     CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGG-G                         --AAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT
genomic: CTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATT

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: 33 (upstream exon), 30 (downstream exon)
Score: 3

ATCTGCGGGACTAGAAGTAATCAAACGGTGTTGCACTTGCGATTGAAAGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttcctt ... tactttgcagGGAAGCATGCCGCTTACAGGTACTCAAGGAAGCGATCGAAAGATCGCGATTGCAGTTGATTTGAGTGATGAAAGTGCCTATGCGGTGAAGTGGGCAGTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGCGGGACTAGAAGTAATCAAACGGTGTTGCACTTGCGATTGAAAGGCTCGGGGGACGGGTTAGGGTTTGTTGGAGTATCGTGTTTTCTATCAGGTGgttgttccttggctccatatttattatttttcgtgttatttttggcgttaacagcttgtgtggctgaagggagaaaaagctacgatgtgtgttggttttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaag