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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAACATGCGACTCAGCATATAGAGGAAGTGAAACCTGATGGTGTAGTGAATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctacttagagtggattcagtctttgagagagagttgctagacaacagataggaatgtgtattataagtgaaagaaatgagaatttgacatcagtc...

Basic information

species Physcomitrella patens
transcript PP1S31_130V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S31_130V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA10G43740.1 (Glycine max), 5'ss of exon 4
CAAACATGCGACTCAGCATATAGAGGAAGTGAAACCTGATGGTGTAGTGAATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctacttagagtggattcagtctttgagagagagttgctagacaacagata-ggaatgtgtattataagtgaaagaaatgagaatttgacatcagtc--
 || |||||   |   ||| | || || || || ||  | ||||| || ||||||||||||||||| || || ||||||||||| || ||| | || |||||||||      || |       ||  | ||  ||   | | |   |    || | | ||  | |    ||  |  |||  ||   | ||     |  ||   
GAAGCATGCTGGTTTTCATCTTGATGAGGTTAAGCCAAAAGGTGTGGTCAATGAGGCTGTGGAACAGATTGCATATGCGGATCGTATAATTGTAAATAAGgtattcagt---gattcatccttgtggtagaatgaatttagttctgctgtggaaatgaaacatttggattatttacaaggcatatcagttatgacttggtaac

upper sequence: PP1S31_130V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT1G80480.1 (Arabidopsis thaliana), 5'ss of exon 4
CAAACATGCGACTCAGCATATAGAGGAAGTGAAACCTGATGGTGTAGTGAATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattcta--cttagagtggattcagtctttgagagagagttgctagacaacagataggaatgtgtattataagtgaaagaaatgagaatttgacatcagtc--
 || |||||   |  |||| |||| || || ||||| || ||||| || ||||||||||| |||||||| |||||||| ||||| || ||  | |||||||||  | |   || ||    | |  ||||   |||||  || | |||        |     || ||  |  ||        |     |  || |  ||  ||  
TAAGCATGCTCGTTTGCATCTAGACGAGGTCAAACCCGAAGGTGTTGTCAATGAGGCTGTTGAACAAATAGCTTATGCAGATCGTATCATAGTTAACAAGgtaaccaaagttttgaacacaatt-gtctcaaagagaatgt-gatagtttttg--tgatcttgagtggttgaatctcttctatcataagattcaggtcgttcct
















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|162253296|gb|FC428890.1|FC428890
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|208374619|gb|DC948619.1|DC948619
EST:     ATGAGGCTG-GGAACNAATCGCTTATGCGGATCGCATTA-TTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|208351971|gb|DC925780.1|DC925780
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162184555|gb|FC360029.1|FC360029
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162156787|gb|FC333599.1|FC333599
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAAATAA-
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAA-TAAA
EST: gi|162253297|gb|FC428891.1|FC428891
EST:     TGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTTGA-CAAG                         ATCGATCTTGTTAAAGAATCTGAGGT
genomic: TGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTT-GAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGT
EST: gi|67725452|gb|BJ975711.1|BJ975711
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162178673|gb|FC354462.1|FC354462
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162195573|gb|FC371874.1|FC371874
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTT
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTT
EST: gi|162155636|gb|FC331561.1|FC331561
EST:     TCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: TCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|208373025|gb|DC948790.1|DC948790
EST:     CGCATTATTTNGAACCAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: CGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162155637|gb|FC331562.1|FC331562
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|37827407|gb|BJ585419.1|BJ585419
EST:     ATCGCATTATTTNGANCAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162162411|gb|FC339168.1|FC339168
EST:     TGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: TGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162162262|gb|FC338044.1|FC338044
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162178674|gb|FC354463.1|FC354463
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162157524|gb|FC333782.1|FC333782
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162187277|gb|FC363227.1|FC363227
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGG
EST: gi|162269789|gb|FC445657.1|FC445657
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
EST: gi|162269788|gb|FC445656.1|FC445656
EST:     ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAG                         ATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG
genomic: ATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG

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), 28 (downstream exon)
Score: 19

CAAACATGCGACTCAGCATATAGAGGAAGTGAAACCTGATGGTGTAGTGAATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctact ... ctcctaacagATCGATCTTGTTAAAGAATCTGAGGTGGAGTCGATGATGCGGCGAATAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAACATGCGACTCAGCATATAGAGGAAGTGAAACCTGATGGTGTAGTGAATGAGGCTGTGGAACAAATCGCTTATGCGGATCGCATTATTTTGAACAAGgtattctacttagagtggattcagtctttgagagagagttgctagacaacagataggaatgtgtattataagtgaaagaaatgagaatttgacatcagtc

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