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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatggttcctgcagaggtcttggagcatgactggggtgtcatatttgtgggtgcttttacaatgagcaggacttatttggatgatgacgtgaatgttgtctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATCATTCCTAGCTCAACTGGAGCTGCAAAG

Basic information

species Physcomitrella patens
transcript PP1S309_84V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S309_84V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 9
gtaatgatggttcctgcagaggtcttggagcatgactggggtgtcatatttgtgggtgcttttacaatgagcaggacttatttggatgatgacgtgaatgttgtctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATCATTCCTAGCTCAACTGGAGCTGCAAAG
     | ||||| |||     |  ||    ||         ||| |  |   | |    ||| |           | | |||   ||||  | || | |||   |  ||| |||||||||||||||| || || || || ||    ||||| ||| | ||||||||||||||||| || ||||| ||||||||||| ||||| || ||||||
-----gttggttactg-----gctttcatccagtgtctacctgttaagtcatttgccattttcatgcattttcaaaataattgtcatgagcatgttactgta--ccatgtccagCCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAG

upper sequence: PP1S309_84V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G16300.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaatgatggttcctgcagaggtcttggagcatgactggggtgtcatatttgtgggtgcttttacaatgagcaggacttatttggatgatgacgtgaatgttgtctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATCATTCCTAGCTCAACTGGAGCTGCAAAG
    |  | | ||||   |   |||||    ||| |     ||| |||||  ||  |  |         |  | |  || |||  |   | |        || |   | | |||| || ||||| |||||||||||||| ||    ||||||||| | ||||| || || ||  | || |||||||||||||||||||| || |||||||||
---gtatttgatccttgtgccctcttgttatatgtc---actgt-atattactgaattttcgagactcaactatgtgttttttttaatcttattctttgcttttgaatattcagCTACTCAGAAAACTGTGGACGGCCCATCAATGAAGGACTGGAGAGGAGGCCGAGGCGCAAGTCAAAACATCATTCCTAGCTCAACAGGCGCTGCAAAG
















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|208388689|gb|DC953451.1|DC953451
EST:     GGCTCATGACCACTGTGCATGCCACCACTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTNGTAAGGACTGGCGTGGAGGAC
genomic: GGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
EST: gi|67725319|gb|BJ975578.1|BJ975578
EST:     GGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
genomic: GGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
EST: gi|208362848|gb|DC950798.1|DC950798
EST:     CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
genomic: CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
EST: gi|208386536|gb|DC952745.1|DC952745
EST:     GGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
genomic: GGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
EST: gi|208388805|gb|DC945381.1|DC945381
EST:     CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCGCTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
genomic: CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
EST: gi|208369277|gb|DC956068.1|DC956068
EST:     CAACTTCGGCANTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
genomic: CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
EST: gi|67723795|gb|BJ974054.1|BJ974054
EST:     GGGCTCATGACCACTGTGCATGCCACCACTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTNGGCGTGGAGGA
genomic: GGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACT-GGCGTGGAGGA
EST: gi|67696731|gb|BJ956964.1|BJ956964
EST:     TCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
genomic: TCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
EST: gi|208361174|gb|DC954280.1|DC954280
EST:     CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
genomic: CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
EST: gi|208361238|gb|DC957707.1|DC957707
EST:     CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC
genomic: CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGAC

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), 26 (downstream exon)
Score: 15

GCCAGTTGCACTACCAACTGTCTTGCACCTCTTGCAAAGGTGATCCAGGACAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATCATTCCTAGCTCAACTGGAGCTGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttacaatgagcaggacttatttggatgatgacgtgaatgttgtctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATCATTCCTAGCTCAACTGGAGCTGCAAAG
                acttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgatggttcctgcagaggtcttggagcatgactggggtgtcatatttgtgggtgcttttacaatgagcaggacttatttggatgatgacgtgaatgttgtctgtgtgcagCCACCCAGAAGACTGTGGACGGCCCGTCTGGTAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATCATTCCTAGCTCAACTGGAGCTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG