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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcctgtgcattccctctataacatcatttcatgctattgcagctttcgaagaaagaacattgaatagttattaacgaaatctttcatttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG

Basic information

species Physcomitrella patens
transcript PP1S79_54V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 13
gtatttcctgtgcattccctctataacatcatttcatgctattgcagctttcgaagaaagaa---cattgaatagttattaacgaaatctttcatt---tttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG
       |  |  |      |  |||  | ||||||| |||  | | |  |  || | |  |     ||  ||  |||||| |   || ||| |     | |  ||||| | || ||||| ||||| |||   ||| ||||    | ||||||||| || || ||||||||||||||||||||||| |||||  | || ||||| |
-----atcaataaaagaaagcagtaat-ttatttcattctaaaggatcagtaaaatagactaatcttttttattattattatcattatttttaaaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 12
-gtatttcctgtgcattccctctataacatcatttcatgctattgcagctttcgaagaaagaacattgaatagttattaacgaaatctttcatt--tttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG
  ||| ||   |  ||       | | ||    || ||   |||  |       |  |||  |   | |||  || ||       ||||| |    | |  ||||| | || ||||| ||||| |||   ||| ||||    | ||||||||| || || ||||||||||||||||||||||| |||||  | || ||||| |
attatgtcagatcaataaaag--aaagcagtgatttatttcattctaaagggtcagtaaaataggct-aatcttttttttttttttcttttaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatttcctgtgcattccctctataacatcatttcatgctattgcagctttcgaagaaagaacattgaatagttattaacgaaatctttcatttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG
         || || |   ||| |      || | ||  | ||  |  ||||  ||  | |||      |  || || |    || ||     |||  ||||  | || || |||||||| |||  |||| ||||   || ||| |||||  | |||||||||||||||||||||||||| |||||  | || ||||| |
---------gt-cacttgatctttttttgtatataatcttcttttatatttcttagttaaaac------tcattttttattcgattttg----tttgcagGGAATTGATGGATCTAGAGTTGAGAAAGTGTTGGAAGCTGTTCACATTGCATCCAACAAAAACACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTG

upper sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 12
--gtatttcctgtgcattccctctataacatcatttcatgctattgcagctttcgaagaaagaacattgaatagttattaacgaaatctttcatttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG
   |||||        ||  ||| ||   ||   |   |  ||||  | ||||      || ||    ||    |||||    |    |||| | | || ||||| | || ||||| ||||| ||    ||| | ||   || ||||||||  || |||||||||||||||||||||||||| || ||  | || ||| | |
aaatatttgagagttgttggctccatttaatttatgtgtattatt-taacttttattataaaaaggaagagccattatttcttatgattttc-tctgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTAGAATCTGTTCATATTGTAGCTAACAAAAACACTGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTG

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|37851231|gb|BJ609239.1|BJ609239
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|162182304|gb|FC357175.1|FC357175
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|37852647|gb|BJ610655.1|BJ610655
EST:     GTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGC
genomic: GTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAA-CCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGC
EST: gi|162155360|gb|FC331766.1|FC331766
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|37845693|gb|BJ603701.1|BJ603701
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|37850584|gb|BJ608592.1|BJ608592
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|37847210|gb|BJ605218.1|BJ605218
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|37850496|gb|BJ608504.1|BJ608504
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|67698707|gb|BJ958940.1|BJ958940
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|208388379|gb|DC949323.1|DC949323
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|37840030|gb|BJ598038.1|BJ598038
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|37838492|gb|BJ596500.1|BJ596500
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|37833067|gb|BJ591079.1|BJ591079
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|67575248|gb|BJ948072.1|BJ948072
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|37838309|gb|BJ596317.1|BJ596317
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
EST: gi|162179834|gb|FC355905.1|FC355905
EST:     TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAG                         GGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG
genomic: TGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCG

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), 34 (downstream exon)
Score: 3

GCCTTGATGAGCCAAGGTTACGAGCTGGTGTCCGGTGGAACAGAGAACCATTTGGTGTTAGTGAACCTCAAACCCAAGgtatttcctg ... atttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctttcgaagaaagaacattgaatagttattaacgaaatctttcatttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG
                            tattaac  putative branch site (score: 3)
                                       tctttcattttttt  putative PPT
                           ttattaacgaaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcctgtgcattccctctataacatcatttcatgctattgcagctttcgaagaaagaacattgaatagttattaacgaaatctttcatttttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG