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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggcttctttaaggttcttttgtagcaattagtttttgggatcacttatctgccacgtagtgtgttatgtcgcttcataacctttaggttggcgaatgttttgacgcag

Basic information

species Physcomitrella patens
transcript PP1S97_259V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S97_259V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA01G41810.1 (Glycine max), 5'ss of exon 2
CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggcttctttaaggttcttttgtagcaattagtttttgggatcac-ttatctgccacgtagtgtgttatgtcgct-tcataacctttaggttggcgaatgttttgacgcag
 | || || || || ||||| ||||||||||| |||||||||||||||   || || ||||||||||||||||||||||| ||||| || || || || |||        | || |||       || | ||  || | ||     ||    |||| |   |   | |   | ||   ||  || |        ||||   |  ||| |||  | ||
AGAGGGCAAACCCCGAAGGTGGCCAAGCAGGATAAGAAGAAGAAGCCACGTGGCCGCGCCCACAAGAGGATGCAGTACAATCGCCGATTCGTCACCGCCGgtat------tcctctaaaccctaattttggc--ttcgattgaataattgtattatgtttgaaaaattagataattgtgcggtctttgatgaggggttttggtttgtgttgttgtag

upper sequence: PP1S97_259V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA05G04670.1 (Glycine max), 5'ss of exon 2
CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtg-cgttggcttc-tttaaggttcttttgtagcaattagtttttgggatcacttatctgccacgtagtgtgttatgtcgcttcataacctttaggttggcgaat---gttttgacgcag------------------------------------------------------------------------
 | || || || ||||| || || ||||| ||||||||||||||||||   || ||||| |||||||| ||||| ||||||||||| || || || || |||  | ||  |||| | |   ||| |  | |     | || |      | |    || | | || |  |  ||| |     ||  |    |||    ||   |||    |||||  |                                                                           
AGAGGACAAACTCCCAAAGTGGCGAAGCAAGACAAGAAGAAGAAGCCACGCGGACGTGCTCACAAGAGAATGCAATACAACCGCCGATTCGTCACCGCCGgtaactttatcttcctctcttgttttcctttgctgttcagatgcctatacccacaatgttcaacatccttagtttttctcttttttccattttctactgaaaaatccgattttgttgtgttagaatagtagagcttgtgaatttggggatttcgtgatatgggttttaattttgatttttgtttgattgtag

upper sequence: PP1S97_259V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv09s0002g02640.t01 (Vitis vinifera), 5'ss of exon 2
CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggcttctttaaggttcttttgtagcaattagtttttgggatcacttatctgccacgtagtgtgttatg-tcgcttcataacctttaggttggcgaatgttttgacgcag
 | || || || || || || ||||| || || |||||||||||||| |  || || || |||||| ||||||||||||||||||| || || || || |||    |    ||| || | |  | |     | |||  ||  | |    | ||  ||  ||  |    | || || | |  |   ||   |       ||                
AGAGGGCAAACCCCAAAAGTCGCCAAACAAGATAAGAAGAAGAAGCCCAGAGGCCGGGCGCACAAGCGGATGCAGTACAACCGCCGTTTCGTCACCGCCGgtaatgttatctctctatgctcatatgacctccattgtttcattgatcaattttgcttgcaaatttcctattctgattggcttgaaaatgtgttccgagc----------------

upper sequence: PP1S97_259V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv11s0016g02690.t01 (Vitis vinifera), 5'ss of exon 2
CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggcttctttaaggttcttttgtagcaattagttt--ttgggatcacttatctgccacgtagtgt-gttatgtcgcttcataacctttaggttggcgaat----gttttgacgcag-------------------------------
 | || || || || || || |||||||| |||||||||||||||||    ||||| || |||||| | ||||| ||||||||||| || || || || |||      |   |  |||      | |  |   || || ||  ||       ||||| |  ||  |    | ||| |   |  | ||     |  | ||    ||     | ||||  |                                  
AGAGGCCAAACCCCAAAAGTGGCCAAGCAAGACAAGAAGAAGAAGCCCCGAGGTCGCGCTCACAAGCGCATGCAATACAACCGCCGATTCGTCACCGCCGgtaaaaacgaaaccctaaatcctatgtagacgtataagatttgtttcatatgcttatttcgcatttgcaatcgttgtcatggataattgaaatgcgattaaaaaactcagggtttgttgtgactgattgtatttcatttgcttttggctgtag

upper sequence: PP1S97_259V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ31630 (Selaginella moellendorffii), 5'ss of exon 2
CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggcttctttaaggttcttttgtagcaattagtttttgggatcacttat-ctgccacgtagtgtgttatgtcgcttcataacctttaggttggcgaatgttttgacgcag
|| || || |||||||||||    ||||||||||||||||||||||| ||||| || || |||||| ||  |||||||||| | || || || || || |||| || |   ||     |  |  |    |||    |     |    ||  | || ||  | | | || | |  |  ||||||      ||   |                     
CGCGGACAAACGCCCAAGGTCCAGAAGCAGGACAAGAAGAAGAAGCCCAAGGGCCGGGCGCACAAGCGGGAGCAGTACAACAGGCGCTTCGTCACGGCGGgtgagtggcaatc-----gcattctcgagagctggaaaagcctccattctttcattctttctccttgtttttgctcacgcttctctcgtttccag---------------------

upper sequence: PP1S97_259V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ30939 (Selaginella moellendorffii), 5'ss of exon 1
CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggcttctttaaggttcttttgtagcaattagtttttgggatcacttatctgccacgtagtgtgttatgtcgcttcataacctttaggttggcgaatgttttgacgcag
|| || ||||||||||||||    ||||||||||||||||||||||| ||||| || || |||||||||  ||| |||||| | || || || || || |||| | | ||   |  ||  | || ||||      | | | ||  | ||||   ||   |    ||                                                 
CGCGGCCAGACGCCCAAGGTCCAGAAGCAGGACAAGAAGAAGAAGCCCAAGGGCCGGGCACACAAGAGGGAGCAATACAACAGGCGATTCGTCACCGCCGgtgagctagcgattgaaatttcctcttgtt----cttgctgtttcgctcacgagtcgcgctttcag-------------------------------------------------

upper sequence: PP1S97_259V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ38518 (Selaginella moellendorffii), 5'ss of exon 2
CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggcttctttaaggttcttttgtagcaattagtttttgggatcacttat-ctgccacgtagtgtgttatgtcgcttcataacctttaggttggcgaatgttttgacgcag
|| || || |||||||||||    ||||||||||||||||||||||| ||||| || || |||||| ||  |||||||||| | || || || || || |||| ||  |  ||     |  |  |    |||    |     |    ||  | || ||  | | | |  | |  |  ||||||      ||   |                     
CGCGGACAAACGCCCAAGGTCCAGAAGCAGGACAAGAAGAAGAAGCCCAAGGGCCGGGCGCACAAGCGGGAGCAGTACAACAGGCGCTTCGTCACGGCGGgtgagtgagaatc-----gcattctcgagagctggaaaagcctccattctttcattctttctccttgcttttgctcacgcttctctcgtttccag---------------------

upper sequence: PP1S97_259V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ17235 (Selaginella moellendorffii), 5'ss of exon 1
CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggcttctttaaggttctt-ttgtagcaattagtttttgggatcacttatctgccacgtagtgtgttatgtcgcttcataacctttaggttggcgaatgttttgacgcag
|| || ||||||||||||||    ||||||||||||||||||||||| ||||| || || |||||||||  ||| |||||| | || || || || || |||| | | ||   |  ||  |||||  |||  |  | |   || | | |  |                                                                
CGCGGCCAGACGCCCAAGGTCCAGAAGCAGGACAAGAAGAAGAAGCCCAAGGGCCGGGCGCACAAGAGGGAGCAATACAACAGGCGATTCGTCACCGCCGgtgagctagcgattgaaattttcttgctgtttcgctcacgattcgcgctttcag--------------------------------------------------------------

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|162274218|gb|FC449978.1|FC449978
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|162278104|gb|FC453923.1|FC453923
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|67692486|gb|BJ952719.1|BJ952719
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|162216409|gb|FC393242.1|FC393242
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|18343785|gb|BJ175823.1|BJ175823
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|67699773|gb|BJ960006.1|BJ960006
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|18335631|gb|BJ167651.1|BJ167651
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|162227643|gb|FC402324.1|FC402324
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|162207654|gb|FC383531.1|FC383531
EST:     CAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: CAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|18347831|gb|BJ179878.1|BJ179878
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|162278103|gb|FC453922.1|FC453922
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|18327360|gb|BJ159362.1|BJ159362
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|18351472|gb|BJ183524.1|BJ183524
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|37830817|gb|BJ588829.1|BJ588829
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|37822977|gb|BJ581043.1|BJ581043
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|67569232|gb|BJ942056.1|BJ942056
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|37826921|gb|BJ584933.1|BJ584933
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
EST: gi|67576266|gb|BJ949090.1|BJ949090
EST:     GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAG                         TGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA
genomic: GGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTA

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), 32 (downstream exon)
Score: 67

CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggc ... tttgacgcagTGGTTGGTTTCGGTAAGAAGAGGGGCCCCAACTCATCGGAGAAGTAGAGTAAGCTGACGGTTGCAAGTCGCCTTACCCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGGTCAGACGCCCAAGGTTGCCAAGCAGGACAAGAAGAAGAAGCCAAAGGGTCGTGCCCACAAGAGGATGCAGTACAACCGCCGGTTTGTGACTGCAGgtgcgttggcttctttaaggttcttttgtagcaattagtttttgggatcacttatctgccacgtagtgtgttatgtcgcttcataacctttaggttggcgaatgttttgacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG