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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttcacttcgaatgcactttagatgttcttggcgcatgtaactttctctgtctggtagagaatcgtattgctggatgtcgtcactgatcgttttgatcgctactctattgttatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACAGGAAGAGCTGGAAATACTGGTATCTCTGTGTTGTTTTACGACAGGAAGA

Basic information

species Physcomitrella patens
transcript PP1S40_169V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S40_169V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv16s0022g02110.t01 (Vitis vinifera), 3'ss of exon 8
gtacttcacttcgaatgcactttagatgttcttggcgcatgta--actttctctgtctggtagagaatcgtattgctggatgtcgtcactgatcgttttgatcgctactctattgttatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACAGGAAGAGCTGGAAATACTGGTATCTCTGTGTTGTTTTACGACAGGAAGA
                   | ||||||||  |    ||||| |  |||  | |      |  | | | |   || |  | | |  |     |      |||| |    | | ||| | |     ||||||| |||||||| ||||  ||| | ||||||||||| ||||| || ||||||||||| |                                       
------------------tcattagatgtaatatatgcatgcatgactaacacaaaaatggtgtggacc---tttcaagttatgcttctcaaatacactgatagtgtttttcttgcttt-----agTGTGAGCCTCCTCGAGATGTTGAAGCTTACATCCATCGATCTGGACGCACAGGAAGAGCAG---------------------------------------
















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|162160197|gb|FC337094.1|FC337094
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
EST: gi|162183859|gb|FC360165.1|FC360165
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
EST: gi|162199364|gb|FC374030.1|FC374030
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
EST: gi|162162672|gb|FC338974.1|FC338974
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
EST: gi|162157788|gb|FC334059.1|FC334059
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
EST: gi|162165912|gb|FC341262.1|FC341262
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
EST: gi|162201473|gb|FC377407.1|FC377407
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGC
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGC
EST: gi|162187537|gb|FC363799.1|FC363799
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
EST: gi|162185256|gb|FC361766.1|FC361766
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
EST: gi|162167302|gb|FC342290.1|FC342290
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGC
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGC
EST: gi|162163230|gb|FC339348.1|FC339348
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGAC
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGAC
EST: gi|162168031|gb|FC344345.1|FC344345
EST:     ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAG                         TGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA
genomic: ATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACA

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: 16

GACACTTCAAGGGTTTCGCACGAGCAAGTTCAGTGTTCTGGTTGCAACGGATGTGGCCGCCAGAGGATTAGACATCAATGACGTTCAGTTGGTGATTCAGgtacttcact ... tatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACAGGAAGAGCTGGAAATACTGGTATCTCTGTGTTGTTTTACGACAGGAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgctggatgtcgtcactgatcgttttgatcgctactctattgttatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACAGGAAGAGCTGGAAATACTGGTATCTCTGTGTTGTTTTACGACAGGAAGA
                                       tattgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttcacttcgaatgcactttagatgttcttggcgcatgtaactttctctgtctggtagagaatcgtattgctggatgtcgtcactgatcgttttgatcgctactctattgttatttggcagTGTGAACCTCCTCGTGATGCCGAAACCTACATCCATCGGTCTGGGCGGACAGGAAGAGCTGGAAATACTGGTATCTCTGTGTTGTTTTACGACAGGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA