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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctgtggattcaacgtgctgcagcaagagaatgctgtagacatttctcgtttacctctaactgattttagaaactgcctttggttttcttccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG

Basic information

species Physcomitrella patens
transcript PP1S49_191V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_191V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 7
agctgtggattcaacgtgctgcagcaagagaatgc-tgtagacatttctcgtttacctctaactgattt-tagaaactgcct--ttggttttcttccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG
      | |      ||| |     || | ||| | |||||   |  ||    || |      |  ||  |||||           |||     |  |   |||| || ||||||||  ||||||| ||  | || ||||| ||||||||||| ||||| || ||||||||| |||||||| |||| ||||||
------gtaccagtagtgat-tgctaataaaatacatgtaggtgtagcttacatatccaagcttcgttaatagaagtcataaaaccggtgaaaatataatgcagGAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAG
















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|162179727|gb|FC356318.1|FC356318
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|208382931|gb|DC923503.1|DC923503
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|162179726|gb|FC356317.1|FC356317
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|37851229|gb|BJ609237.1|BJ609237
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|18334691|gb|BJ166708.1|BJ166708
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|7148089|gb|AW510011.1|AW510011
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATGATGATTCATCAACCTCGTG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTC-TG
EST: gi|162159944|gb|FC336197.1|FC336197
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|18341257|gb|BJ173291.1|BJ173291
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|208381909|gb|DC923433.1|DC923433
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|67696515|gb|BJ956748.1|BJ956748
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|208380837|gb|DC923319.1|DC923319
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|37836163|gb|BJ594171.1|BJ594171
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|162268713|gb|FC445210.1|FC445210
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|208372169|gb|DC947972.1|DC947972
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|37851336|gb|BJ609344.1|BJ609344
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
EST: gi|162259738|gb|FC436744.1|FC436744
EST:     TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAG                         GTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG
genomic: TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGG

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), 35 (downstream exon)
Score: 17

TATGGGAGCTTTTCTCCTTAGTGGTGGCACTAAAGgttcgctttt ... tccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcgtttacctctaactgattttagaaactgcctttggttttcttccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG
                                cctttggttttcttcc  CT-rich tract
                   attttagaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctgtggattcaacgtgctgcagcaagagaatgctgtagacatttctcgtttacctctaactgattttagaaactgcctttggttttcttccatcccagGTAAACGATACAGTCTACCAAATTCGCGAATTATGATTCATCAACCTCTGGGAGGTGCTCAAGGACAGCAGACTGATATTGAAATTCAG

- - - - - - - - tgctgca
- - - - - - - - - - - - - - - - tgctgta