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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG

Basic information

species Physcomitrella patens
transcript PP1S9_103V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
---ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttg-atatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG
   |  | |  |  | | |||| |||  | |||||  | |  |   |||  |   || |       ||| |  || |   || ||  ||||  |   | | |||||||||||||| ||||| ||| ||||||||||    |||||||| |||||||| ||||||||||||||||| |||||||| |||||||| || ||   ||
aatctgtttgttggaat-ccat-gcta-aattgttattttgtttttgcatgtta-tgcttcccagtttggtcatttataaactttttatataacttgtattcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
---------------------------------------------------ccatgtaatcaactaccatagctgtag--ttgttgct-gttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG
                                                   |||||| |    ||  |     | |    |||| |||   | ||  |||   |  |  |   || |    |  ||| |        || | |    | | |||||||||||||||||||| || |||||||| ||    |||||||| || ||||| ||||||||||||||||| || ||||| |||||||| || ||   ||
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttgacattgtagcttaatttgccgcaggcgcata-tgcctttgacagtgcttatcttgtaa-aatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 9
---------ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG
           |   |||    ||   |     ||| |     |  |||    ||  |   || | | || ||| ||| ||||   |  |   ||  ||        ||||||| || || ||||||||  ||||| | ||    | |||||| || ||| |||| |||||||||||||| || ||||||||||||||||| ||   ||
agattatattaaaaaaattgtatagttttttcctagatacctttaatgttctccatgtta-tgatgtttttgttcatatttaatgcaattatgtaaatc--------agGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 9
ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatg-tcgcttgtg-cagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG
  |  | ||     |   |   | ||||| |||||    |    |||| |      |||||      |  ||   |    || ||    |    |    ||||| || || || ||||||||  ||||| | ||    | |||||| || ||| |||| ||||||||||| || || ||||||||||||||||| ||   ||
-aagattatattaaatttttcttttagtttttgctagattccttcaat-gatctacatgttatgatgtttttgttcacatttaatgcaattatgtaaatcagGTGGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGGGGTATAATGAAGTGTGATGTTATAGCAAGTG

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 9
ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG
    ||||  ||  | | |   |    |  |  || ||| ||| || | |  ||  |      ||     ||||  ||  ||  | ||||        |||| |||||||| ||||| || ||||| || |||   | ||||||||| ||  |||||||||| ||||||||||| ||||| |||||||| ||||||  ||
----gtaa--aaggaaccttctttctttcttcacttttgggaatcattggaatgaaa-accaatt-----ttaatagaggtt--tgtgtcaaaaaataagGTGGTGGAAGCGTTTAAGATACTGACATCGGACGATAAAGTGAAAGCAATCTTGGTGAACATATTTGGTGGGATAATGAAATGTGATGTGATTGCTAGTG

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ19055 (Selaginella moellendorffii), 3'ss of exon 9
ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG
                                        | | |  ||        | |||  |      ||  |  | ||  |    |   | | |||||  | ||||| || ||||| || || || |||| ||  ||||| || |||||||||||||| || ||||| |||||||||||| | || || ||   ||
----------------------------------------gtacc--ttataccactttttctctctcgtctagactccgtt--tgctacttctttccagGTCATTGAAGCCTTCAAAATCCTCACGTCTGACAAGAAGGTGAAGGCCATTCTGGTGAACATCTTCGGTGGAATCATGAAGTGTAACGTGATCGCGAGTG

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ13492 (Selaginella moellendorffii), 3'ss of exon 9
ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG
                                            || |       | | |   |      |  ||     ||| ||  ||   | | |||||  | ||||| || ||||| || || || |||| ||  ||||| || |||||||||||||| || ||||| |||||||||||| | || || ||   ||
-----------------------------------------gtacattataccactttttctctctggtctagactctgtttgctacttc---tttccagGTCATTGAAGCCTTCAAAATCCTCACGTCTGACAAGAAGGTGAAGGCCATTCTGGTGAACATCTTCGGTGGAATCATGAAGTGTAACGTGATCGCGAGTG

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|208362322|gb|DC954568.1|DC954568
EST:     GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAG                         GTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
genomic: GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAGgtgtgctttg ... gcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
EST: gi|208364988|gb|DC947130.1|DC947130
EST:     GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAG                         GTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
genomic: GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAGgtgtgctttg ... gcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
EST: gi|208371603|gb|DC952245.1|DC952245
EST:     GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAG                         GTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
genomic: GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAGgtgtgctttg ... gcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
EST: gi|208364115|gb|DC950407.1|DC950407
EST:     GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAG                         GTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
genomic: GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAGgtgtgctttg ... gcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
EST: gi|208366030|gb|DC951125.1|DC951125
EST:     GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAG                         GTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
genomic: GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAGgtgtgctttg ... gcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
EST: gi|37839956|gb|BJ597964.1|BJ597964
EST:     GATGTGGGTGGCAACGCAACTGAGCAACAG                         GTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
genomic: GATGTGGGTGGCAACGCAACTGAGCAACAGgtgtgctttg ... gcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
EST: gi|37840531|gb|BJ598539.1|BJ598539
EST:     GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAG                         GTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT
genomic: GGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAGgtgtgctttg ... gcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATT

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), 33 (downstream exon)
Score: 14

TGGAGCGGGGCTTGCAATGGCTACAATGGATATCATTAAGCTCAGTGGAGGGACCCCTGCCAATTTCTTGGATGTGGGTGGCAACGCAACTGAGCAACAGgtgtgctttg ... gcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG
                     atagttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT