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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataatatttgattttagaatcatcgttttctgtattaaatgttgaccatttttccgctctcatatgtgtcgctagtctctggcgacttgtgctgcc...

Basic information

species Physcomitrella patens
transcript PP1S450_21V6.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S450_21V6.2 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA06G12110.1 (Glycine max), 5'ss of exon 6
GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataat---atttga-ttttagaatcatcgttttctgtattaaatgttgaccatttttccgctctcatatgtgtcgctagtctctggcgacttgtgctgcc
|| || || |||||||| ||  |||||||||| || |||||||| || |||||||||||| | ||||| |||||    |   |||||  ||||| | |||  |||     | |   | |   |                 | | | | | |  |      |  ||  |      
GTTATCTATACAGATGTTGCATTAGATCCTTATTCGTCAGATGGGCATGATGGCATAGTTAGAGAAGATGgtatgctgtcaaatttgtcttttatactcaaagttggaaatctcttaagaaaaatgcaaaagtatataggtttttatagtttattctctacttctcatta----

upper sequence: PP1S450_21V6.2 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA04G42670.1 (Glycine max), 5'ss of exon 7
GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataat---atttga-ttttagaatcatcgttt----tctgtattaaatgttgaccatttttccgctctcatatgtgtcgctagtctctggcgacttgtgctgcc
|| || || |||||||| ||  |||||||||| || |||||||| || |||||||||||| | ||||| |||||   ||   |||||  ||||| | |||  |||     ||| |    ||   ||   |  | |  | | | |||  ||     | |||||    | |||       
GTTATCTATACAGATGTTGCATTAGATCCTTATTCATCAGATGGGCATGATGGCATAGTTAGAGAAGATGgtatgctatcaaatttgtcttttatactcaaagttggaaatctcttgagaaaaatgcagaagtataggtttttatagttg-----attctctttatatttgaatc---
















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|208357191|gb|DC926538.1|DC926538
EST:     GCTAGATCCTTACTNTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|162234870|gb|FC410643.1|FC410643
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|162218487|gb|FC395064.1|FC395064
EST:     AGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: AGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|208353431|gb|DC918487.1|DC918487
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|162234869|gb|FC410642.1|FC410642
EST:     CTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: CTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|100379688|gb|BY949894.1|BY949894
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTTCATCA-CTTTTGCA-GCAGGCCGT
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTT-CATCAACTTT-GCAAGCAGGCCGT
EST: gi|100370598|gb|BY948423.1|BY948423
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGGAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|37852710|gb|BJ610718.1|BJ610718
EST:     CTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: CTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|162268622|gb|FC443676.1|FC443676
EST:     CTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: CTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|162227018|gb|FC403362.1|FC403362
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|162184165|gb|FC359639.1|FC359639
EST:     ATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: ATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|208397366|gb|DC916320.1|DC916320
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|37827165|gb|BJ585177.1|BJ585177
EST:     TTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: TTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|208380828|gb|DC923310.1|DC923310
EST:     GCTAGATCCTTACTNTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|67727441|gb|BJ977700.1|BJ977700
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|162265940|gb|FC442943.1|FC442943
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|208388243|gb|DC945575.1|DC945575
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAG
EST: gi|100357521|gb|BY946437.1|BY946437
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAATGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCGGGCCGTA
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTA
EST: gi|162176323|gb|FC353508.1|FC353508
EST:     GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACG                         GAGTGATTATGAACGACGAGACAGTTCA
genomic: GCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCA

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), 33 (downstream exon)
Score: 9

GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataata ... cctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATTTACACAGATGTGGCGCTAGATCCTTACTCTTCAGATGGTCACGATGGCATAGTTCGGGAAGACGgtatataatatttgattttagaatcatcgttttctgtattaaatgttgaccatttttccgctctcatatgtgtcgctagtctctggcgacttgtgctgcc

- - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA