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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcagggttgagtacgtgcgtgcacgtgtgttggggctggtagtagcgcattggtggttaggcgggatgtatgtggtgcggggaggcgcggaggtgggtgtggcacgtttgtgatggtgggtgtggtgcgattgtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGGGTCGGGCGATGTGCGGCTGCGAGCTGGACATTGTCCGTTATTGGTCTTT

Basic information

species Physcomitrella patens
transcript PP1S348_15V6.1
intron # 6
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|37827533|gb|BJ585545.1|BJ585545
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|162269401|gb|FC445269.1|FC445269
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|162241149|gb|FC417768.1|FC417768
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67725735|gb|BJ975994.1|BJ975994
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67727562|gb|BJ977821.1|BJ977821
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|162207491|gb|FC383736.1|FC383736
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|162241150|gb|FC417769.1|FC417769
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67726117|gb|BJ976376.1|BJ976376
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67726885|gb|BJ977144.1|BJ977144
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|37840320|gb|BJ598328.1|BJ598328
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67722540|gb|BJ972799.1|BJ972799
EST:     GACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACCGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67725283|gb|BJ975542.1|BJ975542
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|208345060|gb|DC925641.1|DC925641
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|208362548|gb|DC943747.1|DC943747
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67716763|gb|BJ967023.1|BJ967023
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|208358628|gb|DC949963.1|DC949963
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|7207565|gb|AW561613.1|AW561613
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|18341253|gb|BJ173287.1|BJ173287
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|37849430|gb|BJ607438.1|BJ607438
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|162249893|gb|FC425694.1|FC425694
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67726399|gb|BJ976658.1|BJ976658
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|162227061|gb|FC402262.1|FC402262
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|37852754|gb|BJ610762.1|BJ610762
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|162227060|gb|FC402261.1|FC402261
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67723293|gb|BJ973552.1|BJ973552
EST:     GTGACGACCANCCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|37830224|gb|BJ588236.1|BJ588236
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|162270400|gb|FC447100.1|FC447100
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|67691435|gb|BJ951668.1|BJ951668
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|208365445|gb|DC950912.1|DC950912
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|18339751|gb|BJ171778.1|BJ171778
EST:     GTNACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|18338400|gb|BJ170424.1|BJ170424
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|162206220|gb|FC382290.1|FC382290
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|37846290|gb|BJ604298.1|BJ604298
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
EST: gi|208354137|gb|DC957385.1|DC957385
EST:     GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAG                         TGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG
genomic: GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGG

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), 34 (downstream exon)
Score: 42

GTGACGACCAACCTAAGGGAGACGACATGAGGCCCGAGGAGGCAGAGgtaatgcagg ... gtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGGGTCGGGCGATGTGCGGCTGCGAGCTGGACATTGTCCGTTATTGGTCTTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcagggttgagtacgtgcgtgcacgtgtgttggggctggtagtagcgcattggtggttaggcgggatgtatgtggtgcggggaggcgcggaggtgggtgtggcacgtttgtgatggtgggtgtggtgcgattgtggatgcagTGACGACGGGGAATGTAAATGCGGAGGAAGGTCGTGACGTGGTCGGGTCGGGTCGGGCGATGTGCGGCTGCGAGCTGGACATTGTCCGTTATTGGTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA