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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAATCCAGAAGATGAAGCCGAAGAGGATGGAGCTAATGTTGACTTGGATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactctccacagaacaacgccttgtgattagcttctgcagcttataactctttcttaatcaatcgatttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaactctaacattatttttggtgaacatacag

Basic information

species Physcomitrella patens
transcript PP1S218_133V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 3
TGTCAATCCAGAAGATGAAGCCGAAGAGGATGGAGCTAATGTTGACTTGGATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgt-actctccacagaacaacgc-cttgtgattagcttctgcagcttataactctttct--taatcaatcgatttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaactctaacattatttttggtgaacatacag
  | || ||||| ||||| || || || ||||| || ||| ||||  | || |||||||||||||| || |||||||| ||||| ||||| |||||||| || |   |   |   |  |  |||   | |||  ||  ||| | ||   || |  |  ||     | | ||| || ||    |  |     | |  ||||                                              
AATGAACCCAGAGGATGACGCAGAGGAAGATGGTGCAAATATTGATCTTGACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagcattttctcattaacatacatgtacttgtcttttacaaggtagagttaattggagcagtaaatggaattttcgaggacctgcagagcaaaa----------------------------------------------
















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|162195316|gb|FC370837.1|FC370837
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|162173415|gb|FC349794.1|FC349794
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|162176626|gb|FC352471.1|FC352471
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100393599|gb|BY953447.1|BY953447
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|208384557|gb|DC915029.1|DC915029
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|208393155|gb|DC907978.1|DC907978
EST:     ATTCTCANAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100386909|gb|BY988178.1|BY988178
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|208367277|gb|DC939835.1|DC939835
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100362918|gb|BY947594.1|BY947594
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|162279775|gb|FC455683.1|FC455683
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|208373514|gb|DC931917.1|DC931917
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|18357560|gb|BJ189619.1|BJ189619
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100423272|gb|BY958215.1|BY958215
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|162260448|gb|FC435061.1|FC435061
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|208351808|gb|DC910362.1|DC910362
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100377926|gb|BY986463.1|BY986463
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|67572938|gb|BJ945762.1|BJ945762
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100445050|gb|BY964349.1|BY964349
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCCTGTAGT-GGTCTAGTGGATCCTGACAGCTTGAAACC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCC-TGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACC
EST: gi|100386534|gb|BY951330.1|BY951330
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|208357259|gb|DC910656.1|DC910656
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|208378607|gb|DC903638.1|DC903638
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100447329|gb|CJ971628.1|CJ971628
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTANTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|162155457|gb|FC330953.1|FC330953
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100445979|gb|CJ970278.1|CJ970278
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|162167872|gb|FC344810.1|FC344810
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100382441|gb|BY969105.1|BY969105
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|162162468|gb|FC339199.1|FC339199
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100386348|gb|BY988015.1|BY988015
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100361517|gb|BY984045.1|BY984045
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100399109|gb|BY954204.1|BY954204
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|162168240|gb|FC344970.1|FC344970
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
EST: gi|100418425|gb|BY957412.1|BY957412
EST:     ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAA                         ACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC
genomic: ATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCC

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: 34 (upstream exon), 31 (downstream exon)
Score: 34

TGTCAATCCAGAAGATGAAGCCGAAGAGGATGGAGCTAATGTTGACTTGGATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactc ... gaacatacagACGATCTTCTTGCCTGTAGTTGGTCTAGTGGATCCTGACAGCTTGAAACCCGGTGACTTGGTTGGAGTAAACAAGGACAGTTATCTAATTCTGGATACAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCAATCCAGAAGATGAAGCCGAAGAGGATGGAGCTAATGTTGACTTGGATTCTCAGAGGAAGGGCAAGTGTGTTGTCTTGAAGACATCCACACGCCAAgtgcgtactctccacagaacaacgccttgtgattagcttctgcagcttataactctttcttaatcaatcgatttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaactctaacattatttttggtgaacatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA