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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACGATCACAAGGTGGACATGCACAATGGTTGCACCTTCAACCATCGCTATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttggtttcctcttggtccaatcgtttcttcgtttgatgttcttgtgctgctagcttttgaagctatgcaagcttcagtttcagaagtttgatcgagtaacccgacgactgctgtttggtttccag

Basic information

species Selaginella moellendorffii
transcript EFJ14577
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14577 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA03G30250.2 (Glycine max), 5'ss of exon 3
CGACGATCACAAGGTGGACATGCACAATGGTTGCACCTTCAACCATCGCTATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttggtttcctcttggtccaatcgtttcttcgtttgatgttct--tgtgctgctagcttttgaagctatgcaagcttcagtttcagaagtttgatcgagtaacccgacgactgctgtttggtttccag
 || ||||||||||| ||||||||  |||| ||||||||||| ||||| ||||||||  | |||||||| ||||| || ||||| || |||||||| || ||||     |||   | |   |  ||| | |     |||||||| | |  ||||||  ||  | |   ||    |     | ||  ||   |  |||  |    |||                          
GGATGATCACAAGGTTGACATGCATGATGGATGCACCTTCAATCATCGATATGTCAAAGCAAATCCACATGAAGTTGAAAATGCCACATGGATGCTAACTgtaa-----gttatttataattataatagctggactgtttgatgatttgatgtgctattatttctcagagtggcgttttttacatgtt---attttttgttatttaat-------------------------

upper sequence: EFJ14577 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA19G33170.1 (Glycine max), 5'ss of exon 3
CGACGATCACAAGGTGGACATGCACAATGGTTGCACCTTCAACCATCGCTATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttggtt------tcctcttggtccaatcgtttcttcgtttgatgttcttgtgctgctagcttttgaagctatgcaagcttcagtttcagaagtttgatcgagtaacccgacgactgctgtttggtttccag
 || ||||||||||| ||||||||  |||| || |||||||| || || ||||||||  | |||||||| ||||| || ||||| || |||||||| || |||| |||  ||      |  | |||| |  |  ||||  |  ||| |||| ||  | ||  | | ||       | | || | |    |||  |   ||| ||                                 
GGATGATCACAAGGTTGACATGCATGATGGATGTACCTTCAATCACCGATATGTCAAAGCAAATCCACATGAAGTTGAAAATGCCACATGGATGCTAACTgtaa-gttatttaatgaattatattggccggactgtttgatgattttatgtgctatttctcatggattggtgttttttacatgtt---atttttgttatttaat---------------------------------

upper sequence: EFJ14577 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv08s0007g06740.t01 (Vitis vinifera), 5'ss of exon 3
CGACGATCACAAGGTGGACATGCACAATGGTTGCACCTTCAACCATCGCTATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttggtttcctcttggtccaatcgtttcttcgtttgatgttcttgtgctgctagc-ttttgaagctatgcaagcttcagtttcagaagtttgatcgagtaacccgacgactgctgtttggtttccag
 |  ||||||||||| ||||||||| |||| || |||||||||||||| |||||||| || ||||| |||||||| || ||||| || |||||||| || |||| |||  |||  || || |  |  | | |   | | || ||||       |   |   |  || |   |||||  ||      |   |  ||   ||   |                            
GGGTGATCACAAGGTTGACATGCACGATGGGTGTACCTTCAACCATCGATATGTCAAATCAAATCCTCAGGAAGTTGAAAATGCCACATGGATGCTAACTgtaa-gtta-ttttatcctgttatatacatatgaacttctgttgtttgatcattttcaatgtgctggaa--atgcatactaagtcattctatattatctcatat----------------------------

upper sequence: EFJ14577 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv06s0004g01130.t01 (Vitis vinifera), 5'ss of exon 2
CGACGATCACAAGGTGGACATGCACAATGGTTGCACCTTCAACCATCGCTATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttggtttcctcttggtccaatcgtttcttcgtttgatgttcttgtgctgctagcttttgaagctatgcaagcttcagtttcagaagtttgatcgagtaacccgacgactgctgtttggtttccag
 || ||||||||||| || |||||  |||| || || ||||||||  | |||||||| |||||||| || |||||||| ||||| || |||||||| || ||||     |    ||||    |  ||  |      |  |||  ||||||      ||  || |  ||||    | | ||   |      |   ||| |||  ||    | ||                  
GGATGATCACAAGGTTGATATGCATGATGGGTGTACTTTCAACCACAGATATGTCAAATCCAATCCCCAAGAAGTCGAAAATGCCACATGGATGCTGACTgtaa-----gacctctctcacacacataat------ggatgactttcttgctacattatgttatttagct---tatgtttggttgctgagaagctgaacgaaaaagaaaaagaa-----------------

upper sequence: EFJ14577 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S35_97V6.1 (Physcomitrella patens), 5'ss of exon 2
CGACGATCACAAGGTGGACATGCACAATGGTTGCACCTTCAACCATCGCTATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttggtttcctcttggtccaatcgtttcttcgtttgatgttcttgtgctgctagcttttgaagctatgcaagcttcagtttcagaagtttgatcgagtaacccgacgactgctgtttggtttccag
 || || ||||| || || ||||||||||| ||||| ||||| ||||||||||| ||||| || ||||| || |||||||| || ||||||||||| |||||||     |    |  |   ||  |  |||||||  | | |  ||  ||    | ||| ||  | |   ||       | | ||  |     |  |||||                              
AGATGAACACAAAGTTGATATGCACAATGGATGCACTTTCAATCATCGCTATGTGAAGTCTAACCCACAAGAGGTCGAGAACGCAACCTGGATGCTAACGgtaataccagcaagccatatctctga--gtttctttttatca-attagtggaaagatagtttgcgtaataatctgcttgtaatttctacgtcctgaatcgaac----------------------------

upper sequence: EFJ14577 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S112_190V6.1 (Physcomitrella patens), 5'ss of exon 2
CGACGATCACAAGGTGGACATGCACAATGGTTGCACCTTCAACCATCGCTATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttggtttcctcttggtccaatcgtttcttcgtttgatgttcttgtgctgctagcttttgaagctatgcaagcttcagtttcagaagtttgatcgagtaacccgacgactgctgtttggtttccag
 || || ||||| || || ||||| ||||| | |||||| || ||||||||||| ||||| |||||||| || |||||||| ||||| |||||||| |||||||          ||||||    | | | |  ||   ||  |  | |||   ||  |  | || | |  |  |||  | || |  |        || | ||                             
AGATGAACACAAAGTTGATATGCATAATGGATTCACCTTTAATCATCGCTATGTGAAGTCTAATCCACAAGAGGTCGAGAACGCTACTTGGATGCTGACGgtaag---------ctcttg-caaactggatgtttgagtttttacttttgaattgagaagtattcatgggaatcaatttgcaatcccgacgtcccgaaccagatgtttac---------------------

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|169050981|gb|FE458151.1|FE458151
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169069800|gb|FE477504.1|FE477504
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169066823|gb|FE473330.1|FE473330
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169066822|gb|FE473329.1|FE473329
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169050980|gb|FE458150.1|FE458150
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169076652|gb|FE485487.1|FE485487
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169018752|gb|FE426729.1|FE426729
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169018751|gb|FE426728.1|FE426728
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169069799|gb|FE477503.1|FE477503
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169033725|gb|FE441653.1|FE441653
EST:     ACGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTATGGACAGCACTTCTGCCTACACTTTGAGGCGTTCCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
EST: gi|169114123|gb|FE516802.1|FE516802
EST:     ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACG                         GTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG
genomic: ATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAG

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: 32 (upstream exon), 30 (downstream exon)
Score: 11

CGACGATCACAAGGTGGACATGCACAATGGTTGCACCTTCAACCATCGCTATGTCAAGTCCAATCCACAGGAAGTCGAGAATGCTACCTGGATGCTCACGgtaacgttgg ... tggtttccagGTTTTCAACTGTTACGGACAGCACTTCTGCCTACACTTTGAGGCGTTTCAGCTCGGGACAATGCCAGTTTACATGGCTTTTTTGAGATTCATGGGGGACG




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