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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagatgtgggcagtttggagtggagagttgtgggggtggtgcgtgtgggtttgtggggttggggacgacgatgacgctgagacggtgtttgtggtgtggtgtgtggtgggtggtgtgtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTGCCACCGAAGCGGCCGCCTGGGCAGTACCATCCGATCCGGTGAAGAAGGG

Basic information

species Physcomitrella patens
transcript PP1S295_30V6.1
intron # 9
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|208354202|gb|DC957422.1|DC957422
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|208392737|gb|DC953634.1|DC953634
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|100414507|gb|BY992807.1|BY992807
EST:     GGATTTGGACGTTCTGTACCATCCCATCTTTGA-CGGCATATACTACACG                         GTTGTGGAGATCATCCCATCAGCTCTTGTTCTGTTTTATTT-GCGGAAGTT
genomic: GGATTTGGACGTTCTGTACCATCCAATCTT-GAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTT-ATTTTGCGGAAGTT
EST: gi|162260165|gb|FC436300.1|FC436300
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|208363026|gb|DC946909.1|DC946909
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|208367886|gb|DC950953.1|DC950953
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|162278111|gb|FC453930.1|FC453930
EST:     GGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGT
genomic: GG-ATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGT
EST: gi|208375008|gb|DC956404.1|DC956404
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|22492481|gb|BU052404.1|BU052404
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGATATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|208358588|gb|DC946549.1|DC946549
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|208396077|gb|DC924543.1|DC924543
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|208374777|gb|DC932046.1|DC932046
EST:     TGGATTTGGACGTNCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTG-GGNA-ANCATCCCATCANCTCTTGTTCTGTT
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGG-AGATCATTCCATCAGCTCTTGTTCTGTT
EST: gi|162278110|gb|FC453929.1|FC453929
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|208361176|gb|DC954282.1|DC954282
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|208399342|gb|DC924772.1|DC924772
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|37845291|gb|BJ603299.1|BJ603299
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|22491854|gb|BU051777.1|BU051777
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
EST: gi|162265852|gb|FC442439.1|FC442439
EST:     TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACG                         GTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG
genomic: TGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTG

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: 26 (upstream exon), 31 (downstream exon)
Score: 5

ATGGCGTTCTCGGTATTCAACAAAGCAATGGATTTGGACGTTCTGTACCATCCAATCTTGAACGGCATATACTACACGgtaagagatg ... gtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTGCCACCGAAGCGGCCGCCTGGGCAGTACCATCCGATCCGGTGAAGAAGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagatgtgggcagtttggagtggagagttgtgggggtggtgcgtgtgggtttgtggggttggggacgacgatgacgctgagacggtgtttgtggtgtggtgtgtggtgggtggtgtgtgcgtgcagGTTGTGGAGATCATTCCATCAGCTCTTGTTCTGTTTATTTTGCGGAAGTTGCCACCGAAGCGGCCGCCTGGGCAGTACCATCCGATCCGGTGAAGAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG